1
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Araúzo-Bravo MJ, Gerovska D, Schwab M, Kretz A. Small extrachromosomal circular DNA in amyotrophic lateral sclerosis matter. Neural Regen Res 2025; 20:1411-1413. [PMID: 39075908 DOI: 10.4103/nrr.nrr-d-23-01877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/25/2024] [Indexed: 07/31/2024] Open
Affiliation(s)
- Marcos J Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastian, Spain (Araúzo-Bravo MJ, Gerovska D)
- Basque Foundation for Science, IKERBASQUE, Bilbao, Spain; Max Planck Institute for Molecular Biomedicine, Computational Biology and Bioinformatics Group, Münster, North Rhine-Westphalia, Germany (Araúzo-Bravo MJ)
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), Leioa, Spain (Araúzo-Bravo MJ)
| | - Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastian, Spain (Araúzo-Bravo MJ, Gerovska D)
| | - Matthias Schwab
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastian, Spain (Araúzo-Bravo MJ, Gerovska D)
- Department of Neurology, Jena University Hospital, Jena, Thuringia, Germany (Schwab M, Kretz A)
| | - Alexandra Kretz
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastian, Spain (Araúzo-Bravo MJ, Gerovska D)
- Department of Neurology, Jena University Hospital, Jena, Thuringia, Germany (Schwab M, Kretz A)
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2
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Keeley O, Coyne AN. Nuclear and degradative functions of the ESCRT-III pathway: implications for neurodegenerative disease. Nucleus 2024; 15:2349085. [PMID: 38700207 PMCID: PMC11073439 DOI: 10.1080/19491034.2024.2349085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024] Open
Abstract
The ESCRT machinery plays a pivotal role in membrane-remodeling events across multiple cellular processes including nuclear envelope repair and reformation, nuclear pore complex surveillance, endolysosomal trafficking, and neuronal pruning. Alterations in ESCRT-III functionality have been associated with neurodegenerative diseases including Frontotemporal Dementia (FTD), Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's Disease (AD). In addition, mutations in specific ESCRT-III proteins have been identified in FTD/ALS. Thus, understanding how disruptions in the fundamental functions of this pathway and its individual protein components in the human central nervous system (CNS) may offer valuable insights into mechanisms underlying neurodegenerative disease pathogenesis and identification of potential therapeutic targets. In this review, we discuss ESCRT components, dynamics, and functions, with a focus on the ESCRT-III pathway. In addition, we explore the implications of altered ESCRT-III function for neurodegeneration with a primary emphasis on nuclear surveillance and endolysosomal trafficking within the CNS.
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Affiliation(s)
- Olivia Keeley
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyssa N. Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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3
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Lin J, Sumara I. Cytoplasmic nucleoporin assemblage: the cellular artwork in physiology and disease. Nucleus 2024; 15:2387534. [PMID: 39135336 PMCID: PMC11323873 DOI: 10.1080/19491034.2024.2387534] [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: 05/08/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/16/2024] Open
Abstract
Nucleoporins, essential proteins building the nuclear pore, are pivotal for ensuring nucleocytoplasmic transport. While traditionally confined to the nuclear envelope, emerging evidence indicates their presence in various cytoplasmic structures, suggesting potential non-transport-related roles. This review consolidates findings on cytoplasmic nucleoporin assemblies across different states, including normal physiological conditions, stress, and pathology, exploring their structural organization, formation dynamics, and functional implications. We summarize the current knowledge and the latest concepts on the regulation of nucleoporin homeostasis, aiming to enhance our understanding of their unexpected roles in physiological and pathological processes.
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Affiliation(s)
- Junyan Lin
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique UMR 7104, Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale U964, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Izabela Sumara
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique UMR 7104, Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale U964, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
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4
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Mallik S, Poch D, Burick S, Schlieker C. Protein folding and quality control during nuclear transport. Curr Opin Cell Biol 2024; 90:102407. [PMID: 39142062 DOI: 10.1016/j.ceb.2024.102407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/06/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024]
Abstract
The spatial separation of protein synthesis from the compartmental destiny of proteins led to the evolution of transport systems that are efficient and yet highly specific. Co-translational transport has emerged as a strategy to avoid cytosolic aggregation of folding intermediates and the need for energy-consuming unfolding strategies to enable transport through narrow conduits connecting compartments. While translation and compartmental translocation are at times tightly coordinated, we know very little about the temporal coordination of translation, protein folding, and nuclear import. Here, we consider the implications of co-translational engagement of nuclear import machinery. We propose that the dynamic interplay of karyopherins and intrinsically disordered nucleoporins create a favorable protein folding environment for cargo en route to the nuclear compartment while maintaining a barrier function of the nuclear pore complex. Our model is discussed in the context of neurological disorders that are tied to defects in nuclear transport and protein quality control.
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Affiliation(s)
- Sunanda Mallik
- Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, CT, USA
| | - Dylan Poch
- Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, CT, USA
| | - Sophia Burick
- Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, CT, USA
| | - Christian Schlieker
- Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, CT, USA; Yale School of Medicine, Department of Cell Biology, New Haven, CT, USA.
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5
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Kim S, Phan S, Tran HT, Shaw TR, Shahmoradian SH, Ellisman MH, Veatch SL, Barmada SJ, Pappas SS, Dauer WT. TorsinA is essential for neuronal nuclear pore complex localization and maturation. Nat Cell Biol 2024:10.1038/s41556-024-01480-1. [PMID: 39117796 DOI: 10.1038/s41556-024-01480-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/11/2024] [Indexed: 08/10/2024]
Abstract
As lifelong interphase cells, neurons face an array of unique challenges. A key challenge is regulating nuclear pore complex (NPC) biogenesis and localization, the mechanisms of which are largely unknown. Here we identify neuronal maturation as a period of strongly upregulated NPC biogenesis. We demonstrate that the AAA+ protein torsinA, whose dysfunction causes the neurodevelopmental movement disorder DYT-TOR1A dystonia and co-ordinates NPC spatial organization without impacting total NPC density. We generated an endogenous Nup107-HaloTag mouse line to directly visualize NPC organization in developing neurons and find that torsinA is essential for proper NPC localization. In the absence of torsinA, the inner nuclear membrane buds excessively at sites of mislocalized nascent NPCs, and the formation of complete NPCs is delayed. Our work demonstrates that NPC spatial organization and number are independently determined and identifies NPC biogenesis as a process vulnerable to neurodevelopmental disease insults.
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Affiliation(s)
- Sumin Kim
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sébastien Phan
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hung Tri Tran
- Peter O'Donnell Jr. Brain Institute, UT Southwestern, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, UT Southwestern, Dallas, TX, USA
| | - Thomas R Shaw
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
- Program in Applied Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Sarah H Shahmoradian
- Peter O'Donnell Jr. Brain Institute, UT Southwestern, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, UT Southwestern, Dallas, TX, USA
- Department of Biophysics, UT Southwestern, Dallas, TX, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sarah L Veatch
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
- Program in Applied Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Sami J Barmada
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, USA.
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
| | - Samuel S Pappas
- Peter O'Donnell Jr. Brain Institute, UT Southwestern, Dallas, TX, USA.
- Department of Neurology, UT Southwestern, Dallas, TX, USA.
| | - William T Dauer
- Peter O'Donnell Jr. Brain Institute, UT Southwestern, Dallas, TX, USA.
- Department of Neurology, UT Southwestern, Dallas, TX, USA.
- Department of Neuroscience, UT Southwestern, Dallas, TX, USA.
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6
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Campbell KR, Hallada LP, Huang YS, Solecki DJ. From Blur to Brilliance: The Ascendance of Advanced Microscopy in Neuronal Cell Biology. Annu Rev Neurosci 2024; 47:235-253. [PMID: 38608643 DOI: 10.1146/annurev-neuro-111020-090208] [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] [Indexed: 04/14/2024]
Abstract
The intricate network of the brain's neurons and synapses poses unparalleled challenges for research, distinct from other biological studies. This is particularly true when dissecting how neurons and their functional units work at a cell biological level. While traditional microscopy has been foundational, it was unable to reveal the deeper complexities of neural interactions. However, an imaging renaissance has transformed our capabilities. Advancements in light and electron microscopy, combined with correlative imaging, now achieve unprecedented resolutions, uncovering the most nuanced neural structures. Maximizing these tools requires more than just technical proficiency. It is crucial to align research aims, allocate resources wisely, and analyze data effectively. At the heart of this evolution is interdisciplinary collaboration, where various experts come together to translate detailed imagery into significant biological insights. This review navigates the latest developments in microscopy, underscoring both the promise of and prerequisites for bending this powerful tool set to understanding neuronal cell biology.
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Affiliation(s)
- Kirby R Campbell
- Neuronal Cell Biology Division, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
| | - Liam P Hallada
- St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Neuronal Cell Biology Division, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
| | - Yu-Shan Huang
- Neuronal Cell Biology Division, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
| | - David J Solecki
- Neuronal Cell Biology Division, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA;
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7
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Chen R, Pathirathna P, Balla RJ, Kim J, Amemiya S. Nanoscale Quantitative Imaging of Single Nuclear Pore Complexes by Scanning Electrochemical Microscopy. Anal Chem 2024; 96:10765-10771. [PMID: 38904303 PMCID: PMC11223102 DOI: 10.1021/acs.analchem.4c01890] [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: 04/10/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/22/2024]
Abstract
The nuclear pore complex (NPC) is a proteinaceous nanopore that solely and selectively regulates the molecular transport between the cytoplasm and nucleus of a eukaryotic cell. The ∼50 nm-diameter pore of the NPC perforates the double-membrane nuclear envelope to mediate both passive and facilitated molecular transport, thereby playing paramount biological and biomedical roles. Herein, we visualize single NPCs by scanning electrochemical microscopy (SECM). The high spatial resolution is accomplished by employing ∼25 nm-diameter ion-selective nanopipets to monitor the passive transport of tetrabutylammonium at individual NPCs. SECM images are quantitatively analyzed by employing the finite element method to confirm that this work represents the highest-resolution nanoscale SECM imaging of biological samples. Significantly, we apply the powerful imaging technique to address the long-debated origin of the central plug of the NPC. Nanoscale SECM imaging demonstrates that unplugged NPCs are more permeable to the small probe ion than are plugged NPCs. This result supports the hypothesis that the central plug is not an intrinsic transporter, but is an impermeable macromolecule, e.g., a ribonucleoprotein, trapped in the nanopore. Moreover, this result also supports the transport mechanism where the NPC is divided into the central pathway for RNA export and the peripheral pathway for protein import to efficiently mediate the bidirectional traffic.
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Affiliation(s)
- Ran Chen
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- School
of Chemistry and Chemical Engineering, Southeast
University, Nanjing 211189, China
| | - Pavithra Pathirathna
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry and Chemical Engineering, Florida
Institute of Technology, Melbourne, Florida 32901, United States
| | - Ryan J. Balla
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jiyeon Kim
- Department
of Chemistry, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Shigeru Amemiya
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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8
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Akter M, Sepehrimanesh M, Xu W, Ding B. Assembling a Coculture System to Prepare Highly Pure Induced Pluripotent Stem Cell-Derived Neurons at Late Maturation Stages. eNeuro 2024; 11:ENEURO.0165-24.2024. [PMID: 39009447 PMCID: PMC11289586 DOI: 10.1523/eneuro.0165-24.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/17/2024] Open
Abstract
Generation of human induced pluripotent stem cell (hiPSC)-derived motor neurons (MNs) offers an unprecedented approach to modeling movement disorders such as dystonia and amyotrophic lateral sclerosis. However, achieving survival poses a significant challenge when culturing induced MNs, especially when aiming to reach late maturation stages. Utilizing hiPSC-derived motor neurons and primary mouse astrocytes, we assembled two types of coculture systems: direct coculturing of neurons with astrocytes and indirect coculture using culture inserts that physically separate neurons and astrocytes. Both systems significantly enhance neuron survival. Compared with these two systems, no significant differences in neurodevelopment, maturation, and survival within 3 weeks, allowing to prepare neurons at maturation stages. Using the indirect coculture system, we obtained highly pure MNs at the late mature stage from hiPSCs. Transcriptomic studies of hiPSC-derived MNs showed a typical neurodevelopmental switch in gene expression from the early immature stage to late maturation stages. Mature genes associated with neurodevelopment and synaptogenesis are highly enriched in MNs at late stages, demonstrating that these neurons achieve maturation. This study introduces a novel tool for the preparation of highly pure hiPSC-derived neurons, enabling the determination of neurological disease pathogenesis in neurons at late disease onset stages through biochemical approaches, which typically necessitate highly pure neurons. This advancement is particularly significant in modeling age-related neurodegeneration.
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Affiliation(s)
- Masuma Akter
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center at Shreveport, Shreveport Louisiana 71130-3932
| | - Masood Sepehrimanesh
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center at Shreveport, Shreveport Louisiana 71130-3932
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette Louisiana 70504
| | - Baojin Ding
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center at Shreveport, Shreveport Louisiana 71130-3932
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Wei Y, Zhou YF, Xiao L, Qin J, Cheng H, Cai H, Chen X, Zou Y, Yang L, Zhang H, Zhang Z, Yang X. Associations of Heavy Metals with Cognitive Function: An Epigenome-Wide View of DNA Methylation and Mediation Analysis. Ann Neurol 2024; 96:87-98. [PMID: 38661228 DOI: 10.1002/ana.26942] [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: 01/13/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024]
Abstract
OBJECTIVE Exposure to heavy metals has been reported to be associated with impaired cognitive function, but the underlying mechanisms remain unclear. This pilot study aimed to identify key heavy metal elements associated with cognitive function and further explore the potential mediating role of metal-related DNA methylation. METHODS Blood levels of arsenic, cadmium, lead, copper, manganese, and zinc and genome-wide DNA methylations were separately detected in peripheral blood in 155 older adults. Cognitive function was evaluated using the Mini-Mental State Examination (MMSE). Least absolute shrinkage and selection operator penalized regression and Bayesian kernel machine regression were used to identify metals associated with cognitive function. An epigenome-wide association study examined the DNA methylation profile of the identified metal, and mediation analysis investigated its mediating role. RESULTS The MMSE scores showed a significant decrease of 1.61 (95% confidence interval [CI]: -2.64, -0.59) with each 1 standard deviation increase in ln-transformed arsenic level; this association was significant in multiple-metal models and dominated the overall negative effect of 6 heavy metal mixture on cognitive function. Seventy-three differentially methylated positions were associated with blood arsenic (p < 1.0 × 10-5). The methylation levels at cg05226051 (annotated to TDRD3) and cg18886932 (annotated to GAL3ST3) mediated 24.8% and 25.5% of the association between blood arsenic and cognitive function, respectively (all p < 0.05). INTERPRETATION Blood arsenic levels displayed a negative association with the cognitive function of older adults. This finding shows that arsenic-related DNA methylation alterations are critical partial mediators that may serve as potential biomarkers for further mechanism-related studies. ANN NEUROL 2024;96:87-98.
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Affiliation(s)
- Yue Wei
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yan-Feng Zhou
- Department of Social Medicine, School of Public Health, Guangxi Medical University, Nanning, China
| | - Lili Xiao
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Jian Qin
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Hong Cheng
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Haiqing Cai
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Xing Chen
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yunfeng Zou
- Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Li Yang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Haiying Zhang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
| | - Zhiyong Zhang
- Department of Environmental Health and Occupational Medicine, Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath Research, Guilin Medical University, Guilin, China
| | - Xiaobo Yang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, China
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10
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Li S, Roy ER, Wang Y, Watkins T, Cao W. DLK-MAPK Signaling Coupled with DNA Damage Promotes Intrinsic Neurotoxicity Associated with Non-Mutated Tau. Mol Neurobiol 2024; 61:2978-2995. [PMID: 37955806 PMCID: PMC11043018 DOI: 10.1007/s12035-023-03720-1] [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: 04/28/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent form of neurodegeneration. Despite the well-established link between tau aggregation and clinical progression, the major pathways driven by this protein to intrinsically damage neurons are incompletely understood. To model AD-relevant neurodegeneration driven by tau, we overexpressed non-mutated human tau in primary mouse neurons and observed substantial axonal degeneration and cell death, a process accompanied by activated caspase 3. Mechanistically, we detected deformation of the nuclear envelope and increased DNA damage response in tau-expressing neurons. Gene profiling analysis further revealed significant alterations in the mitogen-activated protein kinase (MAPK) pathway; moreover, inhibitors of dual leucine zipper kinase (DLK) and c-Jun N-terminal kinase (JNK) were effective in alleviating wild-type human tau-induced neurodegeneration. In contrast, mutant P301L human tau was less toxic to neurons, despite causing comparable DNA damage. Axonal DLK activation induced by wild-type tau potentiated the impact of DNA damage response, resulting in overt neurotoxicity. In summary, we have established a cellular tauopathy model highly relevant to AD and identified a functional synergy between the DLK-MAPK axis and DNA damage response in the neuronal degenerative process.
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Affiliation(s)
- Sanming Li
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Ethan R Roy
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Yanyu Wang
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Trent Watkins
- Department of Neurology, University of California, San Francisco, CA, 94158, USA
| | - Wei Cao
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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11
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Chen Y, Chen X, Luo Z, Kang X, Ge Y, Wan R, Wang Q, Han Z, Li F, Fan Z, Xie Y, Qi B, Zhang X, Yang Z, Zhang JH, Liu D, Xu Y, Wu D, Chen S. Exercise-Induced Reduction of IGF1R Sumoylation Attenuates Neuroinflammation in APP/PS1 Transgenic Mice. J Adv Res 2024:S2090-1232(24)00127-9. [PMID: 38565402 DOI: 10.1016/j.jare.2024.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/03/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024] Open
Abstract
INTRODUCTION Alzheimer's Disease (AD), a progressive neurodegenerative disorder, is marked by cognitive deterioration and heightened neuroinflammation. The influence of Insulin-like Growth Factor 1 Receptor (IGF1R) and its post-translational modifications, especially sumoylation, is crucial in understanding the progression of AD and exploring novel therapeutic avenues. OBJECTIVES This study investigates the impact of exercise on the sumoylation of IGF1R and its role in ameliorating AD symptoms in APP/PS1 mice, with a specific focus on neuroinflammation and innovative therapeutic strategies. METHODS APP/PS1 mice were subjected to a regimen of moderate-intensity exercise. The investigation encompassed assessments of cognitive functions, alterations in hippocampal protein expressions, neuroinflammatory markers, and the effects of exercise on IGF1R and SUMO1 nuclear translocation. Additionally, the study evaluated the efficacy of KPT-330, a nuclear export inhibitor, as an alternative to exercise. RESULTS Exercise notably enhanced cognitive functions in AD mice, possibly through modulations in hippocampal proteins, including Bcl-2 and BACE1. A decrease in neuroinflammatory markers such as IL-1β, IL-6, and TNF-α was observed, indicative of reduced neuroinflammation. Exercise modulated the nuclear translocation of SUMO1 and IGF1R in the hippocampus, thereby facilitating neuronal regeneration. Mutant IGF1R (MT IGF1R), lacking SUMO1 modification sites, showed reduced SUMOylation, leading to diminished expression of pro-inflammatory cytokines and apoptosis. KPT-330 impeded the formation of the IGF1R/RanBP2/SUMO1 complex, thereby limiting IGF1R nuclear translocation, inflammation, and neuronal apoptosis, while enhancing cognitive functions and neuron proliferation. CONCLUSION Moderate-intensity exercise effectively mitigates AD symptoms in mice, primarily by diminishing neuroinflammation, through the reduction of IGF1R Sumoylation. KPT-330, as a potential alternative to physical exercise, enhances the neuroprotective role of IGF1R by inhibiting SUMOylation through targeting XPO1, presenting a promising therapeutic strategy for AD.
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Affiliation(s)
- Yisheng Chen
- Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaofeng Chen
- Department of Orthopaedics, National Regional Medical Center, Jinjiang Municipal Hospital,Shanghai Sixth People's Hospital, Fujian, Jinjiang,China.
| | - Zhiwen Luo
- Huashan Hospital, Fudan University, Shanghai, China
| | - Xueran Kang
- Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, China
| | - Yunshen Ge
- Huashan Hospital, Fudan University, Shanghai, China
| | - Renwen Wan
- Huashan Hospital, Fudan University, Shanghai, China
| | - Qian Wang
- Department of Central Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, Shandong, China
| | - Zhihua Han
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200080, China
| | - Fangqi Li
- Huashan Hospital, Fudan University, Shanghai, China
| | - Zhongcheng Fan
- Department of Orthopaedic Surgery, Hainan Province Clinical Medical Center, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, China
| | - Yuchun Xie
- Jiangsu Province Geriatric Hospital, China
| | - Beijie Qi
- Huashan Hospital, Fudan University, Shanghai, China
| | - Xintao Zhang
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital Lianhua Road, Shenzhen City, Guangdong Province, China
| | - Zhenwei Yang
- Department of Orthopaedics, First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - John H Zhang
- Department of Neurosurgery, Department of Physiology and Pharmacology, Department of Neurosurgery and Anesthesiology, School of Medicine, Loma Linda University, Risley Hall, Room 219, 11041 Campus Street, Loma Linda, CA, 92354, USA.
| | - Danping Liu
- Department of Orthopaedics, First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning Province, China.
| | - Yuzhen Xu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China.
| | - Dongyan Wu
- Huashan Hospital, Fudan University, Shanghai, China.
| | - Shiyi Chen
- Huashan Hospital, Fudan University, Shanghai, China.
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12
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Wu YC, Yan Q, Yue SQ, Pan LX, Yang DS, Tao LS, Wei ZY, Rong F, Qian C, Han MQ, Zuo FC, Yang JF, Xu JJ, Shi ZR, Du J, Chen ZL, Xu T. NUP85 alleviates lipid metabolism and inflammation by regulating PI3K/AKT signaling pathway in nonalcoholic fatty liver disease. Int J Biol Sci 2024; 20:2219-2235. [PMID: 38617542 PMCID: PMC11008257 DOI: 10.7150/ijbs.92337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/10/2024] [Indexed: 04/16/2024] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is one of the common causes of chronic liver disease in the world. The problem of NAFLD had become increasingly prominent. However, its pathogenesis is still indistinct. As we all know, NAFLD begins with the accumulation of triglyceride (TG), leading to fatty degeneration, inflammation and other liver tissues damage. Notably, structure of nucleoporin 85 (NUP85) is related to lipid metabolism and inflammation of liver diseases. In this study, the results of researches indicated that NUP85 played a critical role in NAFLD. Firstly, the expression level of NUP85 in methionine-choline-deficient (MCD)-induced mice increased distinctly, as well as the levels of fat disorder and inflammation. On the contrary, knockdown of NUP85 had the opposite effects. In vitro, AML-12 cells were stimulated with 2 mm free fatty acids (FFA) for 24 h. Results also proved that NUP85 significantly increased in model group, and increased lipid accumulation and inflammation level. Besides, NUP85 protein could interact with C-C motif chemokine receptor 2 (CCR2). Furthermore, when NUP85 protein expressed at an extremely low level, the expression level of CCR2 protein also decreased, accompanied with an inhibition of phosphorylation of phosphoinositol-3 kinase (PI3K)-protein kinase B (AKT) signaling pathway. What is more, trans isomer (ISRIB), a targeted inhibitor of NUP85, could alleviate NAFLD. In summary, our findings suggested that NUP85 functions as an important regulator in NAFLD through modulation of CCR2.
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Affiliation(s)
- Yin-cui Wu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
- Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Qi Yan
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Si-qing Yue
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
- Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Lin-xin Pan
- College of life sciences, Anhui Medical University, Hefei 230032, China
| | - Da-shuai Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
- Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Liang-song Tao
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
- Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Ze-yuan Wei
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
- Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Fan Rong
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
- Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Cheng Qian
- Research and Experiment center, Anhui Medical University, Hefei 230032, China
| | - Meng-qi Han
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
- Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Fu-cheng Zuo
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
- Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Jun-fa Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
- Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
| | - Jia-jia Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Zheng-rong Shi
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jian Du
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Zhao-lin Chen
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui Provincial Hospital, Hefei, Anhui, 230001, China
- Anhui Provincial Key Laboratory of Precision Pharmaceutical Preparations and Clinical Pharmacy, Hefei, Anhui, 230001, China
| | - Tao Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
- Institute for Liver Diseases of Anhui Medical University, Hefei 230032, China
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13
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Qiu Y, Sajidah ES, Kondo S, Narimatsu S, Sandira MI, Higashiguchi Y, Nishide G, Taoka A, Hazawa M, Inaba Y, Inoue H, Matsushima A, Okada Y, Nakada M, Ando T, Lim K, Wong RW. An Efficient Method for Isolating and Purifying Nuclei from Mice Brain for Single-Molecule Imaging Using High-Speed Atomic Force Microscopy. Cells 2024; 13:279. [PMID: 38334671 PMCID: PMC10855070 DOI: 10.3390/cells13030279] [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: 12/20/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/10/2024] Open
Abstract
Nuclear pore complexes (NPCs) on the nuclear membrane surface have a crucial function in controlling the movement of small molecules and macromolecules between the cell nucleus and cytoplasm through their intricate core channel resembling a spiderweb with several layers. Currently, there are few methods available to accurately measure the dynamics of nuclear pores on the nuclear membranes at the nanoscale. The limitation of traditional optical imaging is due to diffraction, which prevents achieving the required resolution for observing a diverse array of organelles and proteins within cells. Super-resolution techniques have effectively addressed this constraint by enabling the observation of subcellular components on the nanoscale. Nevertheless, it is crucial to acknowledge that these methods often need the use of fixed samples. This also raises the question of how closely a static image represents the real intracellular dynamic system. High-speed atomic force microscopy (HS-AFM) is a unique technique used in the field of dynamic structural biology, enabling the study of individual molecules in motion close to their native states. Establishing a reliable and repeatable technique for imaging mammalian tissue at the nanoscale using HS-AFM remains challenging due to inadequate sample preparation. This study presents the rapid strainer microfiltration (RSM) protocol for directly preparing high-quality nuclei from the mouse brain. Subsequently, we promptly utilize HS-AFM real-time imaging and cinematography approaches to record the spatiotemporal of nuclear pore nano-dynamics from the mouse brain.
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Affiliation(s)
- Yujia Qiu
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Elma Sakinatus Sajidah
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
| | - Sota Kondo
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Shinnosuke Narimatsu
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Muhammad Isman Sandira
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Yoshiki Higashiguchi
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Goro Nishide
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Azuma Taoka
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
| | - Masaharu Hazawa
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan
| | - Yuka Inaba
- Metabolism and Nutrition Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-8641, Japan
| | - Hiroshi Inoue
- Metabolism and Nutrition Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-8641, Japan
| | - Ayami Matsushima
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuki Okada
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Mitsutoshi Nakada
- Department of Neurosurgery, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Toshio Ando
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
| | - Keesiang Lim
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
| | - Richard W. Wong
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan
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14
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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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15
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Malik SC, Lin JD, Ziegler-Waldkirch S, Tholen S, Deshpande SS, Schwabenland M, Schilling O, Vlachos A, Meyer-Luehmann M, Schachtrup C. Tpr Misregulation in Hippocampal Neural Stem Cells in Mouse Models of Alzheimer's Disease. Cells 2023; 12:2757. [PMID: 38067185 PMCID: PMC10706632 DOI: 10.3390/cells12232757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/19/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Nuclear pore complexes (NPCs) are highly dynamic macromolecular protein structures that facilitate molecular exchange across the nuclear envelope. Aberrant NPC functioning has been implicated in neurodegeneration. The translocated promoter region (Tpr) is a critical scaffolding nucleoporin (Nup) of the nuclear basket, facing the interior of the NPC. However, the role of Tpr in adult neural stem/precursor cells (NSPCs) in Alzheimer's disease (AD) is unknown. Using super-resolution (SR) and electron microscopy, we defined the different subcellular localizations of Tpr and phospho-Tpr (P-Tpr) in NSPCs in vitro and in vivo. Elevated Tpr expression and reduced P-Tpr nuclear localization accompany NSPC differentiation along the neurogenic lineage. In 5xFAD mice, an animal model of AD, increased Tpr expression in DCX+ hippocampal neuroblasts precedes increased neurogenesis at an early stage, before the onset of amyloid-β plaque formation. Whereas nuclear basket Tpr interacts with chromatin modifiers and NSPC-related transcription factors, P-Tpr interacts and co-localizes with cyclin-dependent kinase 1 (Cdk1) at the nuclear chromatin of NSPCs. In hippocampal NSPCs in a mouse model of AD, aberrant Tpr expression was correlated with altered NPC morphology and counts, and Tpr was aberrantly expressed in postmortem human brain samples from patients with AD. Thus, we propose that altered levels and subcellular localization of Tpr in CNS disease affect Tpr functionality, which in turn regulates the architecture and number of NSPC NPCs, possibly leading to aberrant neurogenesis.
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Affiliation(s)
- Subash C. Malik
- Institute of Anatomy and Cell Biology, University of Freiburg, 79104 Freiburg, Germany; (S.C.M.); (J.-D.L.); (S.S.D.)
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jia-Di Lin
- Institute of Anatomy and Cell Biology, University of Freiburg, 79104 Freiburg, Germany; (S.C.M.); (J.-D.L.); (S.S.D.)
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Stephanie Ziegler-Waldkirch
- Department of Neurology, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (S.Z.-W.); (M.M.-L.)
| | - Stefan Tholen
- Institute of Surgical Pathology, Medical Center, University of Freiburg, 79106 Freiburg, Germany; (S.T.); (O.S.)
| | - Sachin S. Deshpande
- Institute of Anatomy and Cell Biology, University of Freiburg, 79104 Freiburg, Germany; (S.C.M.); (J.-D.L.); (S.S.D.)
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Marius Schwabenland
- Institute of Neuropathology, University of Freiburg, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Medical Center, University of Freiburg, 79106 Freiburg, Germany; (S.T.); (O.S.)
| | - Andreas Vlachos
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany;
- Center BrainLinks-BrainTools, University of Freiburg, 79110 Freiburg, Germany
- Center for Basics in Neuromodulation (NeuroModul Basics), Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Melanie Meyer-Luehmann
- Department of Neurology, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; (S.Z.-W.); (M.M.-L.)
- Center for Basics in Neuromodulation (NeuroModul Basics), Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Christian Schachtrup
- Institute of Anatomy and Cell Biology, University of Freiburg, 79104 Freiburg, Germany; (S.C.M.); (J.-D.L.); (S.S.D.)
- Center for Basics in Neuromodulation (NeuroModul Basics), Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
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16
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Lindell M, Kar D, Sedova A, Kim YJ, Packer OS, Schmidt-Erfurth U, Sloan KR, Marsh M, Dacey DM, Curcio CA, Pollreisz A. Volumetric Reconstruction of a Human Retinal Pigment Epithelial Cell Reveals Specialized Membranes and Polarized Distribution of Organelles. Invest Ophthalmol Vis Sci 2023; 64:35. [PMID: 38133501 PMCID: PMC10746928 DOI: 10.1167/iovs.64.15.35] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/04/2023] [Indexed: 12/23/2023] Open
Abstract
Purpose Despite the centrality of the retinal pigment epithelium (RPE) in vision and retinopathy our picture of RPE morphology is incomplete. With a volumetric reconstruction of human RPE ultrastructure, we aim to characterize major membranous features including apical processes and their interactions with photoreceptor outer segments, basolateral infoldings, and the distribution of intracellular organelles. Methods A parafoveal retinal sample was acquired from a 21-year-old male organ donor. With serial block-face scanning electron microscopy, a tissue volume from the inner-outer segment junction to basal RPE was captured. Surface membranes and complete internal ultrastructure of an individual RPE cell were achieved with a combination of manual and automated segmentation methods. Results In one RPE cell, apical processes constitute 69% of the total cell surface area, through a dense network of over 3000 terminal branches. Single processes contact several photoreceptors. Basolateral infoldings facing the choriocapillaris resemble elongated filopodia and comprise 22% of the cell surface area. Membranous tubules and sacs of endoplasmic reticulum represent 20% of the cell body volume. A dense basal layer of mitochondria extends apically to partly overlap electron-dense pigment granules. Pores in the nuclear envelope form a distinct pattern of rows aligned with chromatin. Conclusions Specialized membranes at the apical and basal side of the RPE cell body involved in intercellular uptake and transport represent over 90% of the total surface area. Together with the polarized distribution of organelles within the cell body, these findings are relevant for retinal clinical imaging, therapeutic approaches, and disease pathomechanisms.
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Affiliation(s)
- Maximilian Lindell
- Department of Ophthalmology, Medical University of Vienna, Vienna, Austria
| | - Deepayan Kar
- Department of Ophthalmology and Visual Sciences, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Aleksandra Sedova
- Department of Ophthalmology, Medical University of Vienna, Vienna, Austria
| | - Yeon Jin Kim
- Department of Biological Structure, University of Washington, Seattle, Washington, United States
| | - Orin S. Packer
- Department of Biological Structure, University of Washington, Seattle, Washington, United States
| | | | - Kenneth R. Sloan
- Department of Ophthalmology and Visual Sciences, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Mike Marsh
- Object Research Systems, Montreal, Quebec, Canada
| | - Dennis M. Dacey
- Department of Biological Structure, University of Washington, Seattle, Washington, United States
| | - Christine A. Curcio
- Department of Ophthalmology and Visual Sciences, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Andreas Pollreisz
- Department of Ophthalmology, Medical University of Vienna, Vienna, Austria
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17
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Yang Y, Guo L, Chen L, Gong B, Jia D, Sun Q. Nuclear transport proteins: structure, function, and disease relevance. Signal Transduct Target Ther 2023; 8:425. [PMID: 37945593 PMCID: PMC10636164 DOI: 10.1038/s41392-023-01649-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 11/12/2023] Open
Abstract
Proper subcellular localization is crucial for the functioning of biomacromolecules, including proteins and RNAs. Nuclear transport is a fundamental cellular process that regulates the localization of many macromolecules within the nuclear or cytoplasmic compartments. In humans, approximately 60 proteins are involved in nuclear transport, including nucleoporins that form membrane-embedded nuclear pore complexes, karyopherins that transport cargoes through these complexes, and Ran system proteins that ensure directed and rapid transport. Many of these nuclear transport proteins play additional and essential roles in mitosis, biomolecular condensation, and gene transcription. Dysregulation of nuclear transport is linked to major human diseases such as cancer, neurodegenerative diseases, and viral infections. Selinexor (KPT-330), an inhibitor targeting the nuclear export factor XPO1 (also known as CRM1), was approved in 2019 to treat two types of blood cancers, and dozens of clinical trials of are ongoing. This review summarizes approximately three decades of research data in this field but focuses on the structure and function of individual nuclear transport proteins from recent studies, providing a cutting-edge and holistic view on the role of nuclear transport proteins in health and disease. In-depth knowledge of this rapidly evolving field has the potential to bring new insights into fundamental biology, pathogenic mechanisms, and therapeutic approaches.
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Affiliation(s)
- Yang Yang
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lu Guo
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lin Chen
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Bo Gong
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China.
| | - Qingxiang Sun
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, China.
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18
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Veldsink AC, Gallardo P, Lusk CP, Veenhoff LM. Changing the guard-nuclear pore complex quality control. FEBS Lett 2023; 597:2739-2749. [PMID: 37715940 DOI: 10.1002/1873-3468.14739] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/18/2023]
Abstract
The integrity of the nuclear envelope depends on the function of nuclear pore complexes (NPCs), transport channels that control macromolecular traffic between the nucleus and cytosol. The central importance of NPCs suggests the existence of quality control (QC) mechanisms that oversee their assembly and function. In this perspective, we emphasize the challenges associated with NPC assembly and the need for QC mechanisms that operate at various stages of an NPC's life. This includes cytosolic preassembly QC that helps enforce key nucleoporin-nucleoporin interactions and their ultimate stoichiometry in the NPC in addition to mechanisms that monitor aberrant fusion of the inner and outer nuclear membranes. Furthermore, we discuss whether and how these QC mechanisms may operate to sense faulty mature NPCs to facilitate their repair or removal. The so far uncovered mechanisms for NPC QC provide fertile ground for future research that not only benefits a better understanding of the vital role that NPCs play in cellular physiology but also how loss of NPC function and/or these QC mechanisms might be an input to aging and disease.
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Affiliation(s)
- Annemiek C Veldsink
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Paola Gallardo
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, CT, New Haven, USA
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
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19
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Theme 05 - Human Cell Biology and Pathology. Amyotroph Lateral Scler Frontotemporal Degener 2023; 24:140-160. [PMID: 37966320 DOI: 10.1080/21678421.2023.2260195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
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20
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Rush C, Jiang Z, Tingey M, Feng F, Yang W. Unveiling the complexity: assessing models describing the structure and function of the nuclear pore complex. Front Cell Dev Biol 2023; 11:1245939. [PMID: 37876551 PMCID: PMC10591098 DOI: 10.3389/fcell.2023.1245939] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/19/2023] [Indexed: 10/26/2023] Open
Abstract
The nuclear pore complex (NPC) serves as a pivotal subcellular structure, acting as a gateway that orchestrates nucleocytoplasmic transport through a selectively permeable barrier. Nucleoporins (Nups), particularly those containing phenylalanine-glycine (FG) motifs, play indispensable roles within this barrier. Recent advancements in technology have significantly deepened our understanding of the NPC's architecture and operational intricacies, owing to comprehensive investigations. Nevertheless, the conspicuous presence of intrinsically disordered regions within FG-Nups continues to present a formidable challenge to conventional static characterization techniques. Historically, a multitude of strategies have been employed to unravel the intricate organization and behavior of FG-Nups within the NPC. These endeavors have given rise to multiple models that strive to elucidate the structural layout and functional significance of FG-Nups. Within this exhaustive review, we present a comprehensive overview of these prominent models, underscoring their proposed dynamic and structural attributes, supported by pertinent research. Through a comparative analysis, we endeavor to shed light on the distinct characteristics and contributions inherent in each model. Simultaneously, it remains crucial to acknowledge the scarcity of unequivocal validation for any of these models, as substantiated by empirical evidence.
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Affiliation(s)
| | | | | | | | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, United States
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Ferreira PA. Nucleocytoplasmic transport at the crossroads of proteostasis, neurodegeneration and neuroprotection. FEBS Lett 2023; 597:2567-2589. [PMID: 37597509 DOI: 10.1002/1873-3468.14722] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/21/2023]
Abstract
Nucleocytoplasmic transport comprises the multistep assembly, transport, and disassembly of protein and RNA cargoes entering and exiting nuclear pores. Accruing evidence supports that impairments to nucleocytoplasmic transport are a hallmark of neurodegenerative diseases. These impairments cause dysregulations in nucleocytoplasmic partitioning and proteostasis of nuclear transport receptors and client substrates that promote intracellular deposits - another hallmark of neurodegeneration. Disturbances in liquid-liquid phase separation (LLPS) between dense and dilute phases of biomolecules implicated in nucleocytoplasmic transport promote micrometer-scale coacervates, leading to proteinaceous aggregates. This Review provides historical and emerging principles of LLPS at the interface of nucleocytoplasmic transport, proteostasis, aging and noxious insults, whose dysregulations promote intracellular aggregates. E3 SUMO-protein ligase Ranbp2 constitutes the cytoplasmic filaments of nuclear pores, where it acts as a molecular hub for rate-limiting steps of nucleocytoplasmic transport. A vignette is provided on the roles of Ranbp2 in nucleocytoplasmic transport and at the intersection of proteostasis in the survival of photoreceptor and motor neurons under homeostatic and pathophysiological environments. Current unmet clinical needs are highlighted, including therapeutics aiming to manipulate aggregation-dissolution models of purported neurotoxicity in neurodegeneration.
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Affiliation(s)
- Paulo A Ferreira
- Department of Ophthalmology, Department of Pathology, Duke University Medical Center, NC, Durham, USA
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22
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Minasbekyan LA, Badalyan HG. Physical model of the nuclear membrane permeability mechanism. Biophys Rev 2023; 15:1195-1207. [PMID: 37974978 PMCID: PMC10643749 DOI: 10.1007/s12551-023-01136-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/31/2023] [Indexed: 11/19/2023] Open
Abstract
Nuclear cytoplasmic transport is mediated by many receptors that recognize specific nuclear localization signals on proteins and RNA and transport these substrates through nuclear pore complexes. Facilitated diffusion through nuclear pore complexes requires the attachment of transport receptors. Despite the relatively large tunnel diameter, some even small proteins (less than 20-30 kDa), such as histones, pass through the nuclear pore complex only with transport receptors. Over several decades, considerable material has been accumulated on the structure, architecture, and amino acid composition of the proteins included in this complex and the sequence of many receptors. We consider the data available in the literature on the structure of the nuclear pore complex and possible mechanisms of nuclear-cytoplasmic transport, applying the theory of electrostatic interactions in the context of our data on changes in the electrokinetic potential of nuclei and our previously proposed physical model of the mechanism of facilitated diffusion through the nuclear pore complex (NPC). According to our data, the main contribution to the charge of the nuclear membrane is made by anionic phospholipids, which are part of both the nuclear membrane and the nuclear matrix, which creates a potential difference between them. The nuclear membrane is a four-layer phospholipid dielectric, so the potential vector can only pass through the NPC, creating an electrostatic funnel that "pulls in" the positively charged load-NLS-NTR trigger complexes. Considering the newly obtained data, an improved model of the previously proposed physical model of the mechanism of nuclear-cytoplasmic transport is proposed. This model considers the contribution of electrostatic fields to the transportation speed when changing the membrane's thickness in the NPC basket at a higher load.
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Affiliation(s)
- Liya A. Minasbekyan
- Scientific Research Institute of Biology, Yerevan State University, A. Manoogian St., 1, 0025 Yerevan, Armenia
| | - Hamlet G. Badalyan
- Chair of General Physics, Yerevan State University, A. Manoogian St., 1, 0025 Yerevan, Armenia
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23
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Cristi AC, Rapuri S, Coyne AN. Nuclear pore complex and nucleocytoplasmic transport disruption in neurodegeneration. FEBS Lett 2023; 597:2546-2566. [PMID: 37657945 PMCID: PMC10612469 DOI: 10.1002/1873-3468.14729] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/29/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
Nuclear pore complexes (NPCs) play a critical role in maintaining the equilibrium between the nucleus and cytoplasm, enabling bidirectional transport across the nuclear envelope, and are essential for proper nuclear organization and gene regulation. Perturbations in the regulatory mechanisms governing NPCs and nuclear envelope homeostasis have been implicated in the pathogenesis of several neurodegenerative diseases. The ESCRT-III pathway emerges as a critical player in the surveillance and preservation of well-assembled, functional NPCs, as well as nuclear envelope sealing. Recent studies have provided insights into the involvement of nuclear ESCRT-III in the selective reduction of specific nucleoporins associated with neurodegenerative pathologies. Thus, maintaining quality control of the nuclear envelope and NPCs represents a pivotal element in the pathological cascade leading to neurodegenerative diseases. This review describes the constituents of the nuclear-cytoplasmic transport machinery, encompassing the nuclear envelope, NPC, and ESCRT proteins, and how their structural and functional alterations contribute to the development of neurodegenerative diseases.
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Affiliation(s)
- América Chandía Cristi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
| | - Sampath Rapuri
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
| | - Alyssa N Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
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24
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Woo E, Bredvik K, Liu B, Fuchs TJ, Manfredi G, Konrad C. Machine learning approaches based on fibroblast morphometry do not predict ALS. Neurobiol Aging 2023; 130:80-83. [PMID: 37473581 DOI: 10.1016/j.neurobiolaging.2023.06.010] [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: 01/02/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neuromuscular disease with limited therapeutic options. Biomarkers are needed for early disease detection, clinical trial design, and personalized medicine. Early evidence suggests that specific morphometric features in ALS primary skin fibroblasts may be used as biomarkers; however, this hypothesis has not been rigorously tested in conclusively large fibroblast populations. Here, we imaged ALS-relevant organelles (mitochondria, endoplasmic reticulum, lysosomes) and proteins (TAR DNA-binding protein 43, Ras GTPase-activating protein-binding protein 1, heat-shock protein 60) at baseline and under stress perturbations and tested their predictive power on a total set of 443 human fibroblast lines from ALS and healthy individuals. Machine learning approaches were able to confidently predict stress perturbation states (ROC-AUC ∼0.99) but not disease groups or clinical features (ROC-AUC 0.58-0.64). Our findings indicate that multivariate models using patient-derived fibroblast morphometry can accurately predict different stressors but are insufficient to develop viable ALS biomarkers.
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Affiliation(s)
- Evan Woo
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Kirsten Bredvik
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Bangyan Liu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Thomas J Fuchs
- Hasso Plattner Institute for Digital Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giovanni Manfredi
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Csaba Konrad
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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25
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Minasbekyan LA, Badalyan HG. Physical model of the nuclear membrane permeability mechanism. Biophys Rev 2023; 15:1195-1207. [DOI: https:/doi.org/10.1007/s12551-023-01136-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/31/2023] [Indexed: 02/27/2024] Open
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Abstract
Orchestration of protein production and degradation and the regulation of protein lifetimes play a central role in many basic biological processes. Nearly all mammalian proteins are replenished by protein turnover in waves of synthesis and degradation. Protein lifetimes in vivo are typically measured in days, but a small number of extremely long-lived proteins (ELLPs) persist for months or even years. ELLPs are rare in all tissues but are enriched in tissues containing terminally differentiated post-mitotic cells and extracellular matrix. Consistently, emerging evidence suggests that the cochlea may be particularly enriched in ELLPs. Damage to ELLPs in specialized cell types, such as crystallin in the lens cells of the eye, causes organ failure such as cataracts. Similarly, damage to cochlear ELLPs is likely to occur with many insults, including acoustic overstimulation, drugs, anoxia, and antibiotics, and may play an underappreciated role in hearing loss. Furthermore, hampered protein degradation may contribute to acquired hearing loss. In this review, I highlight our knowledge of the lifetimes of cochlear proteins with an emphasis on ELLPs and the potential contribution that impaired cochlear protein degradation has on acquired hearing loss and the emerging relevance of ELLPs.
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Affiliation(s)
- Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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27
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McGoldrick P, Robertson J. Unraveling the impact of disrupted nucleocytoplasmic transport systems in C9orf72-associated ALS. Front Cell Neurosci 2023; 17:1247297. [PMID: 37720544 PMCID: PMC10501458 DOI: 10.3389/fncel.2023.1247297] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/08/2023] [Indexed: 09/19/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two adult-onset neurodegenerative diseases that are part of a common disease spectrum due to clinical, genetic, and pathological overlap. A prominent genetic factor contributing to both diseases is a hexanucleotide repeat expansion in a non-coding region of the C9orf72 gene. This mutation in C9orf72 leads to nuclear depletion and cytoplasmic aggregation of Tar DNA-RNA binding protein 43 (TDP-43). TDP-43 pathology is characteristic of the majority of ALS cases, irrespective of disease causation, and is present in ~50% of FTD cases. Defects in nucleocytoplasmic transport involving the nuclear pore complex, the Ran-GTPase cycle, and nuclear transport factors have been linked with the mislocalization of TDP-43. Here, we will explore and discuss the implications of these system abnormalities of nucleocytoplasmic transport in C9orf72-ALS/FTD, as well as in other forms of familial and sporadic ALS.
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Affiliation(s)
- Philip McGoldrick
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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28
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Guo Y, Wang S, Liang F, Wang M. Identification of CHMP7 as a promising immunobiomarker for immunotherapy and chemotherapy and impact on prognosis of colorectal cancer patients. Front Cell Dev Biol 2023; 11:1211843. [PMID: 37711849 PMCID: PMC10499328 DOI: 10.3389/fcell.2023.1211843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/09/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction: ESCRT is a molecular machine involved in various important physiological processes, such as the formation of multivesicular bodies, cellular autophagy, and cellular membrane repair. CHMP7 is a regulatory subunit of ESCRT-III and is necessary for the proper functioning of ESCRT. In this study, public databases were exploited to explore the role of CHMP7 in tumors. Methods: The research on CHMP7 in oncology is rather limited. In this study, the differential expression of CHMP7 in multiple tumor tissues was analyzed with information from public databases and clinically collected colorectal cancer tissue samples. Subsequently, the mutational landscape of CHMP7, methylation levels, and the relationship between its expression levels and genomic instability were resolved. The immune microenvironment is a compelling emerging star in tumor research. The correlation of CHMP7 with various infiltrating immune cell types in TME was analyzed by online datasets and single-cell sequencing. In terms of clinical treatment, the impact of CHMP7 expression levels on chemotherapy and immunotherapy and the evaluation of small molecule drugs related to CHMP7 were assessed. Results: CHMP7 has a predictive value for the prognosis of patients with tumors and is highly involved in tumor immunity. The downregulation of CHMP7 may lead to genomic instability. A strong correlation between CHMP7 and TME immune cell infiltration has been observed, participating in the formation of suppressive TME and promoting tumor progression. The expression level of CHMP7 is significantly lower in the non-responder group of multiple chemotherapeutic agents. CHMP7 can potentially serve as a new biomarker for predicting the efficacy of tumor chemotherapy and immunotherapy. Conclusion: As a gene of interest, CHMP7 is expected to provide novel and promising targets for further treatment of patients with tumor.
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Affiliation(s)
- Yu Guo
- Department of the General Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Shu Wang
- Department of the Ridiotherapy, The Second Hospital of Jilin University, Changchun, China
| | - Feng Liang
- Department of the General Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Min Wang
- Department of the General Surgery, The Second Hospital of Jilin University, Changchun, China
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29
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Martínez-Rojas VA, Pischedda F, Romero-Maldonado I, Khalaf B, Piccoli G, Macchi P, Musio C. Nucleoporin Nup358 Downregulation Tunes the Neuronal Excitability in Mouse Cortical Neurons. Life (Basel) 2023; 13:1791. [PMID: 37763196 PMCID: PMC10533191 DOI: 10.3390/life13091791] [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: 06/16/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Nucleoporins (NUPs) are proteins that comprise the nuclear pore complexes (NPCs). The NPC spans the nuclear envelope of a cell and provides a channel through which RNA and proteins move between the nucleus and the cytoplasm and vice versa. NUP and NPC disruptions have a great impact on the pathophysiology of neurodegenerative diseases (NDDs). Although the downregulation of Nup358 leads to a reduction in the scaffold protein ankyrin-G at the axon initial segment (AIS) of mature neurons, the function of Nup358 in the cytoplasm of neurons remains elusive. To investigate whether Nup358 plays any role in neuronal activity, we downregulated Nup358 in non-pathological mouse cortical neurons and measured their active and passive bioelectrical properties. We identified that Nup358 downregulation is able to produce significant modifications of cell-membrane excitability via voltage-gated sodium channel kinetics. Our findings suggest that Nup358 contributes to neuronal excitability through a functional stabilization of the electrical properties of the neuronal membrane. Hypotheses will be discussed regarding the alteration of this active regulation as putatively occurring in the pathophysiology of NDDs.
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Affiliation(s)
| | - Francesca Pischedda
- Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (F.P.); (B.K.); (G.P.)
| | - Isabel Romero-Maldonado
- Institute of Cellular Physiology, Universidad Autónoma de Mexico—UNAM, Ciudad Universitaria, Mexico City 04510, Mexico;
| | - Bouchra Khalaf
- Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (F.P.); (B.K.); (G.P.)
| | - Giovanni Piccoli
- Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (F.P.); (B.K.); (G.P.)
| | - Paolo Macchi
- Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy; (F.P.); (B.K.); (G.P.)
| | - Carlo Musio
- Institute of Biophysics—IBF, National Research Council—CNR, Via Sommarive 18, 38123 Trento, Italy;
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30
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Dos Passos PM, Hemamali EH, Mamede LD, Hayes LR, Ayala YM. RNA-mediated ribonucleoprotein assembly controls TDP-43 nuclear retention. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.06.552215. [PMID: 37609278 PMCID: PMC10441353 DOI: 10.1101/2023.08.06.552215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
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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31
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Forgham H, Liu L, Zhu J, Javed I, Cai W, Qiao R, Davis TP. Vector enabled CRISPR gene editing - A revolutionary strategy for targeting the diversity of brain pathologies. Coord Chem Rev 2023; 487:215172. [PMID: 37305445 PMCID: PMC10249757 DOI: 10.1016/j.ccr.2023.215172] [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] [Indexed: 06/13/2023]
Abstract
Brain pathologies are considered one of the greatest contributors of death and disability worldwide. Neurodegenerative Alzheimer's disease is the second leading cause of death in adults, whilst brain cancers including glioblastoma multiforme in adults, and pediatric-type high-grade gliomas in children remain largely untreatable. A further compounding issue for patients with brain pathologies is that of long-term neuropsychiatric sequela - as a symptom or arising from high dose therapeutic intervention. The major challenge to effective, low dose treatment is finding therapeutics that successfully cross the blood-brain barrier and target aberrant cellular processes, while having minimum effect on essential cellular processes, and healthy bystander cells. Following over 30 years of research, CRISPR technology has emerged as a biomedical tour de force with the potential to revolutionise the treatment of both neurological and cancer related brain pathologies. The aim of this review is to take stock of the progress made in CRISPR technology in relation to treating brain pathologies. Specifically, we will describe studies which look beyond design, synthesis, and theoretical application; and focus instead on in vivo studies with translation potential. Along with discussing the latest breakthrough techniques being applied within the CRISPR field, we aim to provide a prospective on the knowledge gaps that exist and challenges that still lay ahead for CRISPR technology prior to successful application in the brain disease treatment field.
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Affiliation(s)
- Helen Forgham
- Australian Institute of Bioengineering & Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Liwei Liu
- Australian Institute of Bioengineering & Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jiayuan Zhu
- Australian Institute of Bioengineering & Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ibrahim Javed
- Australian Institute of Bioengineering & Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Weibo Cai
- Departments of Radiology and Medical Physics, University of Wisconsin – Madison, Madison, WI, USA
| | - Ruirui Qiao
- Australian Institute of Bioengineering & Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas P. Davis
- Australian Institute of Bioengineering & Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
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32
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Traxler L, Lucciola R, Herdy JR, Jones JR, Mertens J, Gage FH. Neural cell state shifts and fate loss in ageing and age-related diseases. Nat Rev Neurol 2023; 19:434-443. [PMID: 37268723 PMCID: PMC10478103 DOI: 10.1038/s41582-023-00815-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2023] [Indexed: 06/04/2023]
Abstract
Most age-related neurodegenerative diseases remain incurable owing to an incomplete understanding of the disease mechanisms. Several environmental and genetic factors contribute to disease onset, with human biological ageing being the primary risk factor. In response to acute cellular damage and external stimuli, somatic cells undergo state shifts characterized by temporal changes in their structure and function that increase their resilience, repair cellular damage, and lead to their mobilization to counteract the pathology. This basic cell biological principle also applies to human brain cells, including mature neurons that upregulate developmental features such as cell cycle markers or glycolytic reprogramming in response to stress. Although such temporary state shifts are required to sustain the function and resilience of the young human brain, excessive state shifts in the aged brain might result in terminal fate loss of neurons and glia, characterized by a permanent change in cell identity. Here, we offer a new perspective on the roles of cell states in sustaining health and counteracting disease, and we examine how cellular ageing might set the stage for pathological fate loss and neurodegeneration. A better understanding of neuronal state and fate shifts might provide the means for a controlled manipulation of cell fate to promote brain resilience and repair.
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Affiliation(s)
- Larissa Traxler
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Raffaella Lucciola
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Herdy
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jeffrey R Jones
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jerome Mertens
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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33
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Cowburn D, Rout M. Improving the hole picture: towards a consensus on the mechanism of nuclear transport. Biochem Soc Trans 2023; 51:871-886. [PMID: 37099395 PMCID: PMC10212546 DOI: 10.1042/bst20220494] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/27/2023]
Abstract
Nuclear pore complexes (NPCs) mediate the exchange of materials between the nucleoplasm and cytoplasm, playing a key role in the separation of nucleic acids and proteins into their required compartments. The static structure of the NPC is relatively well defined by recent cryo-EM and other studies. The functional roles of dynamic components in the pore of the NPC, phenylalanyl-glycyl (FG) repeat rich nucleoporins, is less clear because of our limited understanding of highly dynamic protein systems. These proteins form a 'restrained concentrate' which interacts with and concentrates nuclear transport factors (NTRs) to provide facilitated nucleocytoplasmic transport of cargoes. Very rapid on- and off-rates among FG repeats and NTRs supports extremely fast facilitated transport, close to the rate of macromolecular diffusion in cytoplasm, while complexes without specific interactions are entropically excluded, though details on several aspects of the transport mechanism and FG repeat behaviors remain to be resolved. However, as discussed here, new technical approaches combined with more advanced modeling methods will likely provide an improved dynamic description of NPC transport, potentially at the atomic level in the near future. Such advances are likely to be of major benefit in comprehending the roles the malfunctioning NPC plays in cancer, ageing, viral diseases, and neurodegeneration.
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Affiliation(s)
- David Cowburn
- Departments of Biochemistry and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| | - Michael Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, U.S.A
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34
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Kozai T, Fernandez-Martinez J, van Eeuwen T, Gallardo P, Kapinos LE, Mazur A, Zhang W, Tempkin J, Panatala R, Delgado-Izquierdo M, Raveh B, Sali A, Chait BT, Veenhoff LM, Rout MP, Lim RYH. Dynamic molecular mechanism of the nuclear pore complex permeability barrier. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535055. [PMID: 37066338 PMCID: PMC10103940 DOI: 10.1101/2023.03.31.535055] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Nuclear pore complexes (NPCs) mediate nucleocytoplasmic transport of specific macromolecules while impeding the exchange of unsolicited material. However, key aspects of this gating mechanism remain controversial. To address this issue, we determined the nanoscopic behavior of the permeability barrier directly within yeast S. cerevisiae NPCs at transport-relevant timescales. We show that the large intrinsically disordered domains of phenylalanine-glycine repeat nucleoporins (FG Nups) exhibit highly dynamic fluctuations to create transient voids in the permeability barrier that continuously shape-shift and reseal, resembling a radial polymer brush. Together with cargo-carrying transport factors the FG domains form a feature called the central plug, which is also highly dynamic. Remarkably, NPC mutants with longer FG domains show interweaving meshwork-like behavior that attenuates nucleocytoplasmic transport in vivo. Importantly, the bona fide nanoscale NPC behaviors and morphologies are not recapitulated by in vitro FG domain hydrogels. NPCs also exclude self-assembling FG domain condensates in vivo, thereby indicating that the permeability barrier is not generated by a self-assembling phase condensate, but rather is largely a polymer brush, organized by the NPC scaffold, whose dynamic gating selectivity is strongly enhanced by the presence of transport factors.
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Affiliation(s)
- Toshiya Kozai
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940, Leioa, Spain
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
| | - Paola Gallardo
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Netherlands
| | | | - Adam Mazur
- Biozentrum, University of Basel, Switzerland
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, U.S.A
| | - Jeremy Tempkin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, U.S.A. Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | | | - Barak Raveh
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, U.S.A. Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, U.S.A
| | - Liesbeth M. Veenhoff
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Netherlands
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
| | - Roderick Y. H. Lim
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
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Kumar MS, Stallworth KM, Murthy AC, Lim SM, Li N, Jain A, Munro JB, Fawzi NL, Lagier-Tourenne C, Bosco DA. Interactions between FUS and the C-terminal Domain of Nup62 are Sufficient for their Co-phase Separation into Amorphous Assemblies. J Mol Biol 2023; 435:167972. [PMID: 36690069 PMCID: PMC10329203 DOI: 10.1016/j.jmb.2023.167972] [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: 09/08/2022] [Revised: 12/29/2022] [Accepted: 01/15/2023] [Indexed: 01/22/2023]
Abstract
Deficient nucleocytoplasmic transport is emerging as a pathogenic feature of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), including in ALS caused by mutations in Fused in Sarcoma (FUS). Recently, both wild-type and ALS-linked mutant FUS were shown to directly interact with the phenylalanine-glycine (FG)-rich nucleoporin 62 (Nup62) protein, where FUS WT/ Nup62 interactions were enriched within the nucleus but ALS-linked mutant FUS/ Nup62 interactions were enriched within the cytoplasm of cells. Nup62 is a central channel Nup that has a prominent role in forming the selectivity filter within the nuclear pore complex and in regulating effective nucleocytoplasmic transport. Under conditions where FUS phase separates into liquid droplets in vitro, the addition of Nup62 caused the synergistic formation of amorphous assemblies containing both FUS and Nup62. Here, we examined the molecular determinants of this process using recombinant FUS and Nup62 proteins and biochemical approaches. We demonstrate that the structured C-terminal domain of Nup62 containing an alpha-helical coiled-coil region plays a dominant role in binding FUS and is sufficient for inducing the formation of FUS/Nup62 amorphous assemblies. In contrast, the natively unstructured, F/G repeat-rich N-terminal domain of Nup62 modestly contributed to FUS/Nup62 phase separation behavior. Expression of individual Nup62 domain constructs in human cells confirmed that the Nup62 C-terminal domain is essential for localization of the protein to the nuclear envelope. Our results raise the possibility that interactions between FUS and the C-terminal domain of Nup62 can influence the function of Nup62 under physiological and/or pathological conditions.
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Affiliation(s)
- Meenakshi Sundaram Kumar
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, MA 01605, USA; Biochemistry and Molecular Biotechnology Program, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Karly M Stallworth
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, MA 01605, USA
| | - Anastasia C Murthy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Su Min Lim
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nan Li
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Aastha Jain
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James B Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Daryl A Bosco
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, MA 01605, USA.
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Li S, Roy ER, Wang Y, Watkins T, Cao W. Modeling Alzheimer's disease in primary neurons reveals DNA damage response coupled with MAPK-DLK signaling in wild-type tau-induced neurodegeneration. RESEARCH SQUARE 2023:rs.3.rs-2617457. [PMID: 36945524 PMCID: PMC10029119 DOI: 10.21203/rs.3.rs-2617457/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Background Alzheimer's disease (AD) is the most prevalent form of neurodegeneration. Despite the well-established link between tau aggregation and clinical progression, the major pathways driven by this protein to intrinsically damage neurons are incompletely understood. Methods To model AD-relevant neurodegeneration driven by tau, we overexpressed wild-type human tau in primary mouse neurons and characterized the subsequent cellular and molecular changes. RNAseq profiling and functional investigation were performed as well. A direct comparison with a mutant human tau was conducted in detail. Results We observed substantial axonal degeneration and cell death associated with wild-type tau, a process accompanied by activated caspase 3. Mechanistically, we detected deformation of the nuclear envelope and increased DNA damage response in tau-expressing neurons. Gene profiling analysis further revealed significant alterations in the mitogen-activated protein kinase (MAPK) pathway; moreover, inhibitors of dual leucine zipper kinase (DLK) and c-Jun N-terminal kinase (JNK) were effective in alleviating wild-type human tau-induced neurodegeneration. In contrast, mutant P301L human tau was less toxic to neurons, despite causing comparable DNA damage. Axonal DLK activation induced by wild-type tau potentiated the impact of DNA damage response, resulting in overt neurotoxicity. Conclusions We have established a cellular tauopathy model highly relevant to AD and identified a functional synergy between DNA damage response and the MAPK-DLK axis in the neuronal degenerative process.
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Affiliation(s)
- Sanming Li
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ethan R Roy
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yanyu Wang
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Trent Watkins
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA. Current address: Department of Neurology, University of California at San Francisco, San Francisco, CA 94158 USA
| | - Wei Cao
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Zhu X, Qi C, Wang R, Lee JH, Shao J, Bei L, Xiong F, Nguyen PT, Li G, Krakowiak J, Koh SP, Simon LM, Han L, Moore TI, Li W. Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization. Cell Rep 2022; 41:111576. [PMID: 36323253 PMCID: PMC9744245 DOI: 10.1016/j.celrep.2022.111576] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/26/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
The nuclear pore complex (NPC) comprises more than 30 nucleoporins (NUPs) and is a hallmark of eukaryotes. NUPs have been suggested to be important in regulating gene transcription and 3D genome organization. However, evidence in support of their direct roles remains limited. Here, by Cut&Run, we find that core NUPs display broad but also cell-type-specific association with active promoters and enhancers in human cells. Auxin-mediated rapid depletion of two NUPs demonstrates that NUP93, but not NUP35, directly and specifically controls gene transcription. NUP93 directly activates genes with high levels of RNA polymerase II loading and transcriptional elongation by facilitating full BRD4 recruitment to their active enhancers. dCas9-based tethering confirms a direct and causal role of NUP93 in gene transcriptional activation. Unexpectedly, in situ Hi-C and H3K27ac or H3K4me1 HiChIP results upon acute NUP93 depletion show negligible changesS2211-1247(22)01437-1 of 3D genome organization ranging from A/B compartments and topologically associating domains (TADs) to enhancer-promoter contacts.
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Affiliation(s)
- Xiaoyu Zhu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA,These authors contributed equally
| | - Chuangye Qi
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA,These authors contributed equally
| | - Ruoyu Wang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA,The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA,These authors contributed equally
| | - Joo-Hyung Lee
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jiaofang Shao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lanxin Bei
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA,The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Phuoc T. Nguyen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA,The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Guojie Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Joanna Krakowiak
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Su-Pin Koh
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Lukas M. Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Travis I. Moore
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA,The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA,Lead contact,Correspondence:
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Inagaki E, Yoshimatsu S, Okano H. Accelerated neuronal aging in vitro ∼melting watch ∼. Front Aging Neurosci 2022; 14:868770. [PMID: 36016855 PMCID: PMC9397486 DOI: 10.3389/fnagi.2022.868770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
In developed countries, the aging of the population and the associated increase in age-related diseases are causing major unresolved medical, social, and environmental matters. Therefore, research on aging has become one of the most important and urgent issues in life sciences. If the molecular mechanisms of the onset and progression of neurodegenerative diseases are elucidated, we can expect to develop disease-modifying methods to prevent neurodegeneration itself. Since the discovery of induced pluripotent stem cells (iPSCs), there has been an explosion of disease models using disease-specific iPSCs derived from patient-derived somatic cells. By inducing the differentiation of iPSCs into neurons, disease models that reflect the patient-derived pathology can be reproduced in culture dishes, and are playing an active role in elucidating new pathological mechanisms and as a platform for new drug discovery. At the same time, however, we are faced with a new problem: how to recapitulate aging in culture dishes. It has been pointed out that cells differentiated from pluripotent stem cells are juvenile, retain embryonic traits, and may not be fully mature. Therefore, attempts are being made to induce cell maturation, senescence, and stress signals through culture conditions. It has also been reported that direct conversion of fibroblasts into neurons can reproduce human neurons with an aged phenotype. Here, we outline some state-of-the-art insights into models of neuronal aging in vitro. New frontiers in which stem cells and methods for inducing differentiation of tissue regeneration can be applied to aging research are just now approaching, and we need to keep a close eye on them. These models are forefront and intended to advance our knowledge of the molecular mechanisms of aging and contribute to the development of novel therapies for human neurodegenerative diseases associated with aging.
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Affiliation(s)
- Emi Inagaki
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
- Japanese Society for the Promotion of Science (JSPS), Tokyo, Japan
| | - Sho Yoshimatsu
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
- *Correspondence: Hideyuki Okano,
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