1
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Song J. Molecular Mechanisms of Phase Separation and Amyloidosis of ALS/FTD-linked FUS and TDP-43. Aging Dis 2024; 15:2084-2112. [PMID: 38029395 PMCID: PMC11346406 DOI: 10.14336/ad.2023.1118] [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: 08/01/2023] [Accepted: 11/18/2023] [Indexed: 12/01/2023] Open
Abstract
FUS and TDP-43, two RNA-binding proteins from the heterogeneous nuclear ribonucleoprotein family, have gained significant attention in the field of neurodegenerative diseases due to their association with amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). They possess folded domains for binding ATP and various nucleic acids including DNA and RNA, as well as substantial intrinsically disordered regions (IDRs) including prion-like domains (PLDs) and RG-/RGG-rich regions. They play vital roles in various cellular processes, including transcription, splicing, microRNA maturation, RNA stability and transport and DNA repair. In particular, they are key components for forming ribonucleoprotein granules and stress granules (SGs) through homotypic or heterotypic liquid-liquid phase separation (LLPS). Strikingly, liquid-like droplets formed by FUS and TDP-43 may undergo aging to transform into less dynamic assemblies such as hydrogels, inclusions, and amyloid fibrils, which are the pathological hallmarks of ALS and FTD. This review aims to synthesize and consolidate the biophysical knowledge of the sequences, structures, stability, dynamics, and inter-domain interactions of FUS and TDP-43 domains, so as to shed light on the molecular mechanisms underlying their liquid-liquid phase separation (LLPS) and amyloidosis. The review further delves into the mechanisms through which ALS-causing mutants of the well-folded hPFN1 disrupt the dynamics of LLPS of FUS prion-like domain, providing key insights into a potential mechanism for misfolding/aggregation-prone proteins to cause neurodegenerative diseases and aging by gain of functions. With better understanding of different biophysical aspects of FUS and TDP-43, the ultimate goal is to develop drugs targeting LLPS and amyloidosis, which could mediate protein homeostasis within cells and lead to new treatments for currently intractable diseases, particularly neurodegenerative diseases such as ALS, FTD and aging. However, the study of membrane-less organelles and condensates is still in its infancy and therefore the review also highlights key questions that require future investigation.
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2
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Hayashi M, Girdhar A, Ko YH, Kim KM, DePierro JA, Buchler JR, Arunprakash N, Bajaj A, Cingolani G, Guo L. Engineered NLS-chimera downregulates expression of aggregation-prone endogenous FUS. Nat Commun 2024; 15:7887. [PMID: 39251571 DOI: 10.1038/s41467-024-52151-6] [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: 12/08/2023] [Accepted: 08/27/2024] [Indexed: 09/11/2024] Open
Abstract
Importin β-superfamily nuclear import receptors (NIRs) mitigate mislocalization and aggregation of RNA-binding proteins (RBPs), like FUS and TDP-43, which are implicated in neurodegenerative diseases. NIRs potently disaggregate RBPs by recognizing their nuclear localization signal (NLS). However, disease-causing mutations in NLS compromise NIR binding and activity. Here, we define features that characterize the anti-aggregation activity of NIR and NLS. We find that high binding affinity between NIR and NLS, and optimal NLS location relative to the aggregating domain plays a role in determining NIR disaggregation activity. A designed FUS chimera (FUSIBB), carrying the importin β binding (IBB) domain, is solubilized by importin β in vitro, translocated to the nucleus in cultured cells, and downregulates the expression of endogenous FUS. In this study, we posit that guiding the mutual recognition of NLSs and NIRs will aid the development of therapeutics, illustrated by the highly soluble FUSIBB replacing the aggregation-prone endogenous FUS.
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Affiliation(s)
- Miyuki Hayashi
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Amandeep Girdhar
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ying-Hui Ko
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kevin M Kim
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jacquelyn A DePierro
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Joseph R Buchler
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Nikhita Arunprakash
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Aditya Bajaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Lin Guo
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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3
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Hoover SC, Margossian KO, Muthukumar M. Theory and quantitative assessment of pH-responsive polyzwitterion-polyelectrolyte complexation. SOFT MATTER 2024. [PMID: 39222025 DOI: 10.1039/d4sm00575a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
We introduce a theoretical framework to describe the pH-sensitive phase behavior of polyzwitterion-polyelectrolyte complex coacervates that reasonably captures the phenomenon from recent experimental observations. The polyzwitterion is described by a combinatorial sequence of the four states in which each zwitterionic monomer can occupy: dipolar, quasi-cationic, quasi-anionic, and fully neutralized. We explore the effects of various modifiable chemical and physical properties of the polymers-such as, pKa of the pH-active charged group on the zwitterion, equilibrium constant of salt condensation on the permanently charged group on the zwitterion, degrees of polymerization, hydrophobicity (via the Flory-Huggins interaction parameter), and dipole lengths-on the window of complexation across many stoichiometric mixing ratios of polyzwitterion and polyelectrolyte. The properties that determine the net charge of the polyzwitterion have the strongest effect on the pH range in which polyzwitterion-polyelectrolyte complexation occurs. We finish with general guidance for those interested in molecular design of polyzwitterion-polyelectrolyte complex coacervates and opportunities for future investigation.
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Affiliation(s)
- Samuel C Hoover
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Khatcher O Margossian
- Department of Polymer Science and Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA.
- Rush University Medical Center and John H. Stroger Hospital of Cook County, both in Chicago, IL 60612, USA
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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4
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Boyd-Shiwarski CR, Shiwarski DJ, Subramanya AR. A New Phase for WNK Kinase Signaling Complexes as Biomolecular Condensates. Physiology (Bethesda) 2024; 39:0. [PMID: 38624245 DOI: 10.1152/physiol.00013.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024] Open
Abstract
The purpose of this review is to highlight transformative advances that have been made in the field of biomolecular condensates, with special emphasis on condensate material properties, physiology, and kinases, using the With-No-Lysine (WNK) kinases as a prototypical example. To convey how WNK kinases illustrate important concepts for biomolecular condensates, we start with a brief history, focus on defining features of biomolecular condensates, and delve into some examples of how condensates are implicated in cellular physiology (and pathophysiology). We then highlight how WNK kinases, through the action of "WNK droplets" that ubiquitously regulate intracellular volume and kidney-specific "WNK bodies" that are implicated in distal tubule salt reabsorption and potassium homeostasis, exemplify many of the defining features of condensates. Finally, this review addresses the controversies within this emerging field and questions to address.
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Affiliation(s)
- Cary R Boyd-Shiwarski
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Pittsburgh Heart, Lung, Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Daniel J Shiwarski
- Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Arohan R Subramanya
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Pittsburgh Heart, Lung, Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, United States
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5
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Vieira de Sá R, Sudria-Lopez E, Cañizares Luna M, Harschnitz O, van den Heuvel DMA, Kling S, Vonk D, Westeneng HJ, Karst H, Bloemenkamp L, Varderidou-Minasian S, Schlegel DK, Mars M, Broekhoven MH, van Kronenburg NCH, Adolfs Y, Vangoor VR, de Jongh R, Ljubikj T, Peeters L, Seeler S, Mocholi E, Basak O, Gordon D, Giuliani F, Verhoeff T, Korsten G, Calafat Pla T, Venø MT, Kjems J, Talbot K, van Es MA, Veldink JH, van den Berg LH, Zelina P, Pasterkamp RJ. ATAXIN-2 intermediate-length polyglutamine expansions elicit ALS-associated metabolic and immune phenotypes. Nat Commun 2024; 15:7484. [PMID: 39209824 PMCID: PMC11362472 DOI: 10.1038/s41467-024-51676-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
Intermediate-length repeat expansions in ATAXIN-2 (ATXN2) are the strongest genetic risk factor for amyotrophic lateral sclerosis (ALS). At the molecular level, ATXN2 intermediate expansions enhance TDP-43 toxicity and pathology. However, whether this triggers ALS pathogenesis at the cellular and functional level remains unknown. Here, we combine patient-derived and mouse models to dissect the effects of ATXN2 intermediate expansions in an ALS background. iPSC-derived motor neurons from ATXN2-ALS patients show altered stress granules, neurite damage and abnormal electrophysiological properties compared to healthy control and other familial ALS mutations. In TDP-43Tg-ALS mice, ATXN2-Q33 causes reduced motor function, NMJ alterations, neuron degeneration and altered in vitro stress granule dynamics. Furthermore, gene expression changes related to mitochondrial function and inflammatory response are detected and confirmed at the cellular level in mice and human neuron and organoid models. Together, these results define pathogenic defects underlying ATXN2-ALS and provide a framework for future research into ATXN2-dependent pathogenesis and therapy.
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Affiliation(s)
- Renata Vieira de Sá
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Emma Sudria-Lopez
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Marta Cañizares Luna
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Oliver Harschnitz
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CX, Utrecht, The Netherlands
- Human Technopole, Viale Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Dianne M A van den Heuvel
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Sandra Kling
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Danielle Vonk
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Henk-Jan Westeneng
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CX, Utrecht, The Netherlands
| | - Henk Karst
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Lauri Bloemenkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Suzy Varderidou-Minasian
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Domino K Schlegel
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Mayte Mars
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Mark H Broekhoven
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Nicky C H van Kronenburg
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Youri Adolfs
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Vamshidhar R Vangoor
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Rianne de Jongh
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Tijana Ljubikj
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Lianne Peeters
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Sabine Seeler
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Enric Mocholi
- Center for Molecuar Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Onur Basak
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - David Gordon
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, UK
| | - Fabrizio Giuliani
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CX, Utrecht, The Netherlands
| | - Tessa Verhoeff
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Giel Korsten
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Teresa Calafat Pla
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Morten T Venø
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Omiics ApS, Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford, UK
| | - Michael A van Es
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CX, Utrecht, The Netherlands
| | - Jan H Veldink
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CX, Utrecht, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CX, Utrecht, The Netherlands
| | - Pavol Zelina
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands.
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6
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Alirzayeva H, Loureiro R, Koyuncu S, Hommen F, Nabawi Y, Zhang WH, Dao TTP, Wehrmann M, Lee HJ, Vilchez D. ALS-FUS mutations cause abnormal PARylation and histone H1.2 interaction, leading to pathological changes. Cell Rep 2024; 43:114626. [PMID: 39167487 DOI: 10.1016/j.celrep.2024.114626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/13/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
The majority of severe early-onset and juvenile cases of amyotrophic lateral sclerosis (ALS) are caused by mutations in the FUS gene, resulting in rapid disease progression. Mutant FUS accumulates within stress granules (SGs), thereby affecting the dynamics of these ribonucleoprotein complexes. Here, we define the interactome of the severe mutant FUSP525L variant in human induced pluripotent stem cell (iPSC)-derived motor neurons. We find increased interaction of FUSP525L with the PARP1 enzyme, promoting poly-ADP-ribosylation (PARylation) and binding of FUS to histone H1.2. Inhibiting PARylation or reducing H1.2 levels alleviates mutant FUS aggregation, SG alterations, and apoptosis in human motor neurons. Conversely, elevated H1.2 levels exacerbate FUS-ALS phenotypes, driven by the internally disordered terminal domains of H1.2. In C. elegans models, knockdown of H1.2 and PARP1 orthologs also decreases FUSP525L aggregation and neurodegeneration, whereas H1.2 overexpression worsens ALS-related changes. Our findings indicate a link between PARylation, H1.2, and FUS with potential therapeutic implications.
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Affiliation(s)
- Hafiza Alirzayeva
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Rute Loureiro
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Seda Koyuncu
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Franziska Hommen
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Yara Nabawi
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - William Hongyu Zhang
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Thien T P Dao
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Markus Wehrmann
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Hyun Ju Lee
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - David Vilchez
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
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7
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Sun J, Chen Y, Bi R, Yuan Y, Yu H. Bioinformatic approaches of liquid-liquid phase separation in human disease. Chin Med J (Engl) 2024; 137:1912-1925. [PMID: 39033393 PMCID: PMC11332758 DOI: 10.1097/cm9.0000000000003249] [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: 04/28/2024] [Indexed: 07/23/2024] Open
Abstract
ABSTRACT Biomolecular aggregation within cellular environments via liquid-liquid phase separation (LLPS) spontaneously forms droplet-like structures, which play pivotal roles in diverse biological processes. These structures are closely associated with a range of diseases, including neurodegenerative disorders, cancer and infectious diseases, highlighting the significance of understanding LLPS mechanisms for elucidating disease pathogenesis, and exploring potential therapeutic interventions. In this review, we delineate recent advancements in LLPS research, emphasizing its pathological relevance, therapeutic considerations, and the pivotal role of bioinformatic tools and databases in facilitating LLPS investigations. Additionally, we undertook a comprehensive analysis of bioinformatic resources dedicated to LLPS research in order to elucidate their functionality and applicability. By providing comprehensive insights into current LLPS-related bioinformatics resources, this review highlights its implications for human health and disease.
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Affiliation(s)
- Jun Sun
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yilong Chen
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ruiye Bi
- Department of Orthognathic and TMJ Surgery, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yong Yuan
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, Sichuan 610041, China
| | - Haopeng Yu
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, Sichuan 610041, China
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8
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Cui Q, Liu Z, Bai G. Friend or foe: The role of stress granule in neurodegenerative disease. Neuron 2024; 112:2464-2485. [PMID: 38744273 DOI: 10.1016/j.neuron.2024.04.025] [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: 12/01/2023] [Revised: 03/12/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024]
Abstract
Stress granules (SGs) are dynamic membraneless organelles that form in response to cellular stress. SGs are predominantly composed of RNA and RNA-binding proteins that assemble through liquid-liquid phase separation. Although the formation of SGs is considered a transient and protective response to cellular stress, their dysregulation or persistence may contribute to various neurodegenerative diseases. This review aims to provide a comprehensive overview of SG physiology and pathology. It covers the formation, composition, regulation, and functions of SGs, along with their crosstalk with other membrane-bound and membraneless organelles. Furthermore, this review discusses the dual roles of SGs as both friends and foes in neurodegenerative diseases and explores potential therapeutic approaches targeting SGs. The challenges and future perspectives in this field are also highlighted. A more profound comprehension of the intricate relationship between SGs and neurodegenerative diseases could inspire the development of innovative therapeutic interventions against these devastating diseases.
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Affiliation(s)
- Qinqin Cui
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Nanhu Brain-Computer Interface Institute, Hangzhou 311100, China.
| | - Zongyu Liu
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ge Bai
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Nanhu Brain-Computer Interface Institute, Hangzhou 311100, China; Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, State Key Laboratory of Brain-Machine Intelligence, Zhejiang University, Hangzhou 311121, China; NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou 310058, China; Institute of Fundamental and Transdisciplinary Research, Zhejiang University, Hangzhou 310058, China.
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9
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Owens MC, Yanas A, Liu KF. Sex chromosome-encoded protein homologs: current progress and open questions. Nat Struct Mol Biol 2024; 31:1156-1166. [PMID: 39123067 DOI: 10.1038/s41594-024-01362-y] [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: 04/28/2023] [Accepted: 06/28/2024] [Indexed: 08/12/2024]
Abstract
The complexity of biological sex differences is markedly evident in human physiology and pathology. Although many of these differences can be ascribed to the expression of sex hormones, another contributor to sex differences lies in the sex chromosomes beyond their role in sex determination. Although largely nonhomologous, the human sex chromosomes express seventeen pairs of homologous genes, referred to as the 'X-Y pairs.' The X chromosome-encoded homologs of these Y-encoded proteins are crucial players in several cellular processes, and their dysregulation frequently results in disease development. Many diseases related to these X-encoded homologs present with sex-biased incidence or severity. By contrast, comparatively little is known about the differential functions of the Y-linked homologs. Here, we summarize and discuss the current understanding of five of these X-Y paired proteins, with recent evidence of differential functions and of having a potential link to sex biases in disease, highlighting how amino acid-level sequence differences may differentiate their functions and contribute to sex biases in human disease.
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Affiliation(s)
- Michael C Owens
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Amber Yanas
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Institute for RNA Innovation, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA, USA.
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10
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Lindamood HL, Liu TM, Read TA, Vitriol EA. Using ALS to understand profilin 1's diverse roles in cellular physiology. Cytoskeleton (Hoboken) 2024. [PMID: 39056295 DOI: 10.1002/cm.21896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024]
Abstract
Profilin is an actin monomer-binding protein whose role in actin polymerization has been studied for nearly 50 years. While its principal biochemical features are now well understood, many questions remain about how profilin controls diverse processes within the cell. Dysregulation of profilin has been implicated in a broad range of human diseases, including neurodegeneration, inflammatory disorders, cardiac disease, and cancer. For example, mutations in the profilin 1 gene (PFN1) can cause amyotrophic lateral sclerosis (ALS), although the precise mechanisms that drive neurodegeneration remain unclear. While initial work suggested proteostasis and actin cytoskeleton defects as the main pathological pathways, multiple novel functions for PFN1 have since been discovered that may also contribute to ALS, including the regulation of nucleocytoplasmic transport, stress granules, mitochondria, and microtubules. Here, we will review these newly discovered roles for PFN1, speculate on their contribution to ALS, and discuss how defects in actin can contribute to these processes. By understanding profilin 1's involvement in ALS pathogenesis, we hope to gain insight into this functionally complex protein with significant influence over cellular physiology.
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Affiliation(s)
- Halli L Lindamood
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Tatiana M Liu
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Tracy-Ann Read
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Eric A Vitriol
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
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11
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Majumder S, Coupe S, Fakhri N, Jain A. Sequence programmable nucleic acid coacervates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.22.604687. [PMID: 39091847 PMCID: PMC11291106 DOI: 10.1101/2024.07.22.604687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Nature uses bottom-up self-assembly to build structures with remarkable complexity and functionality. Understanding how molecular-scale interactions translate to macroscopic properties remains a major challenge and requires systems that effectively bridge these two scales. Here, we generate DNA and RNA liquids with exquisite programmability in their material properties. Nucleic acids are negatively charged, and in the presence of polycations, they may condense to a liquid-like state. Within these liquids, DNA and RNA retain sequence-specific hybridization abilities. We show that intermolecular hybridization in the condensed phase cross-links molecules and slows down chain dynamics. This reduced chain mobility is mirrored in the macroscopic properties of the condensates. Molecular diffusivity and material viscosity scale with the intermolecular hybridization energy, enabling precise sequence-based modulation of condensate properties over orders of magnitude. Our work offers a robust platform to create self-assembling programmable fluids and may help advance our understanding of liquid-like compartments in cells.
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Affiliation(s)
- Sumit Majumder
- Whitehead Institute for Biomedical Research, Cambridge 02142, USA
| | - Sebastian Coupe
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, USA
| | - Nikta Fakhri
- Department of Physics, Massachusetts Institute of Technology, Cambridge 02142, USA
| | - Ankur Jain
- Whitehead Institute for Biomedical Research, Cambridge 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, USA
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12
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Zhang W, Li Z, Wang X, Sun T. Phase separation is regulated by post-translational modifications and participates in the developments of human diseases. Heliyon 2024; 10:e34035. [PMID: 39071719 PMCID: PMC11279762 DOI: 10.1016/j.heliyon.2024.e34035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) of intracellular proteins has emerged as a hot research topic in recent years. Membrane-less and liquid-like condensates provide dense spaces that ensure cells to high efficiently regulate genes transcription and rapidly respond to burst changes from the environment. The fomation and activity of LLPS are not only modulated by the cytosol conditions including but not limited to salt concentration and temperture. Interestingly, recent studies have shown that phase separation is also regulated by various post-translational modifications (PTMs) through modulating proteins multivalency, such as solubility and charge interactions. The regulation mechanism is crucial for normal functioning of cells, as aberrant protein aggregates are often closely related with the occurrence and development of human diseases including cancer and nurodegenerative diseases. Therefore, studying phase separation in the perspective of protein PTMs has long-term significance for human health. In this review, we summarized the properties and cellular physiological functions of LLPS, particularly its relationships with PTMs in human diseases according to recent researches.
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Affiliation(s)
- Weibo Zhang
- Faculty of Health Sciences Building University of Macau E12 Avenida da Universidade, Taipa, Macau, China
| | - Zhengfeng Li
- Faculty of Health Sciences Building University of Macau E12 Avenida da Universidade, Taipa, Macau, China
| | - Xianju Wang
- Faculty of Health Sciences Building University of Macau E12 Avenida da Universidade, Taipa, Macau, China
| | - Ting Sun
- Faculty of Health Sciences Building University of Macau E12 Avenida da Universidade, Taipa, Macau, China
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13
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Chuang HY, He RY, Huang YA, Hsu WT, Cheng YJ, Guo ZR, Wali N, Hwang IS, Shie JJ, Huang JJT. Engineered droplet-forming peptide as photocontrollable phase modulator for fused in sarcoma protein. Nat Commun 2024; 15:5686. [PMID: 38971830 PMCID: PMC11227587 DOI: 10.1038/s41467-024-50025-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 06/27/2024] [Indexed: 07/08/2024] Open
Abstract
The assembly and disassembly of biomolecular condensates are crucial for the subcellular compartmentalization of biomolecules in the control of cellular reactions. Recently, a correlation has been discovered between the phase transition of condensates and their maturation (aggregation) process in diseases. Therefore, modulating the phase of condensates to unravel the roles of condensation has become a matter of interest. Here, we create a peptide-based phase modulator, JSF1, which forms droplets in the dark and transforms into amyloid-like fibrils upon photoinitiation, as evidenced by their distinctive nanomechanical and dynamic properties. JSF1 is found to effectively enhance the condensation of purified fused in sarcoma (FUS) protein and, upon light exposure, induce its fibrilization. We also use JSF1 to modulate the biophysical states of FUS condensates in live cells and elucidate the relationship between FUS phase transition and FUS proteinopathy, thereby shedding light on the effect of protein phase transition on cellular function and malfunction.
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Affiliation(s)
- Hao-Yu Chuang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Ruei-Yu He
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Yung-An Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Wan-Ting Hsu
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Ya-Jen Cheng
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, 115, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Zheng-Rong Guo
- Institute of Physics, Academia Sinica, Taipei, 115, Taiwan
| | - Niaz Wali
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | | | - Jiun-Jie Shie
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Joseph Jen-Tse Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, 115, Taiwan.
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
- Department of Applied Chemistry, National Chiayi University, Chiayi City, 600, Taiwan.
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14
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D'Antoni S, Spatuzza M, Bonaccorso CM, Catania MV. Role of fragile X messenger ribonucleoprotein 1 in the pathophysiology of brain disorders: a glia perspective. Neurosci Biobehav Rev 2024; 162:105731. [PMID: 38763180 DOI: 10.1016/j.neubiorev.2024.105731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
Fragile X messenger ribonucleoprotein 1 (FMRP) is a widely expressed RNA binding protein involved in several steps of mRNA metabolism. Mutations in the FMR1 gene encoding FMRP are responsible for fragile X syndrome (FXS), a leading genetic cause of intellectual disability and autism spectrum disorder, and fragile X-associated tremor-ataxia syndrome (FXTAS), a neurodegenerative disorder in aging men. Although FMRP is mainly expressed in neurons, it is also present in glial cells and its deficiency or altered expression can affect functions of glial cells with implications for the pathophysiology of brain disorders. The present review focuses on recent advances on the role of glial subtypes, astrocytes, oligodendrocytes and microglia, in the pathophysiology of FXS and FXTAS, and describes how the absence or reduced expression of FMRP in these cells can impact on glial and neuronal functions. We will also briefly address the role of FMRP in radial glial cells and its effects on neural development, and gliomas and will speculate on the role of glial FMRP in other brain disorders.
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Affiliation(s)
- S D'Antoni
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Via Paolo Gaifami 18, Catania 95126, Italy
| | - M Spatuzza
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Via Paolo Gaifami 18, Catania 95126, Italy
| | - C M Bonaccorso
- Oasi Research Institute - IRCCS, via Conte Ruggero 73, Troina 94018, Italy
| | - M V Catania
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Via Paolo Gaifami 18, Catania 95126, Italy.
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15
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Sprunger ML, Jackrel ME. The role of Matrin-3 in physiology and its dysregulation in disease. Biochem Soc Trans 2024; 52:961-972. [PMID: 38813817 PMCID: PMC11209761 DOI: 10.1042/bst20220585] [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: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
The dysfunction of many RNA-binding proteins (RBPs) that are heavily disordered, including TDP-43 and FUS, are implicated in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). These proteins serve many important roles in the cell, and their capacity to form biomolecular condensates (BMCs) is key to their function, but also a vulnerability that can lead to misregulation and disease. Matrin-3 (MATR3) is an intrinsically disordered RBP implicated both genetically and pathologically in ALS/FTD, though it is relatively understudied as compared with TDP-43 and FUS. In addition to binding RNA, MATR3 also binds DNA and is implicated in many cellular processes including the DNA damage response, transcription, splicing, and cell differentiation. It is unclear if MATR3 localizes to BMCs under physiological conditions, which is brought further into question due to its lack of a prion-like domain. Here, we review recent studies regarding MATR3 and its roles in numerous physiological processes, as well as its implication in a range of diseases.
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Affiliation(s)
- Macy L Sprunger
- Department of Chemistry, Washington University, St. Louis, MO 63130, U.S.A
| | - Meredith E Jackrel
- Department of Chemistry, Washington University, St. Louis, MO 63130, U.S.A
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16
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Garai S, Raizada A, Kumar V, Sopory SK, Pareek A, Singla-Pareek SL, Kaur C. In silico analysis of fungal prion-like proteins for elucidating their role in plant-fungi interactions. Arch Microbiol 2024; 206:308. [PMID: 38896139 DOI: 10.1007/s00203-024-04040-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/21/2024]
Abstract
Prion-like proteins (PrLPs) have emerged as beneficial molecules with implications in adaptive responses. These proteins possess a conserved prion-like domain (PrLD) which is an intrinsically disordered region capable of adopting different conformations upon perceiving external stimuli. Owing to changes in protein conformation, functional characteristics of proteins harboring PrLDs get altered thereby, providing a unique mode of protein-based regulation. Since PrLPs are ubiquitous in nature and involved in diverse functions, through this study, we aim to explore the role of such domains in yet another important physiological process viz. plant-microbe interactions to get insights into the mechanisms dictating cross-kingdom interactions. We have evaluated the presence and functions of PrLPs in 18 different plant-associated fungi of agricultural importance to unravel their role in plant-microbe interactions. Of the 241,997 proteins scanned, 3,820 (~ 1.6%) were identified as putative PrLPs with pathogenic fungi showing significantly higher PrLP density than their beneficial counterparts. Further, through GO enrichment analysis, we could predict several PrLPs from pathogenic fungi to be involved in virulence and formation of stress granules. Notably, PrLPs involved in (retro)transposition were observed exclusively in pathogenic fungi. We even analyzed publicly available data for the expression alterations of fungal PrLPs upon their interaction with their respective hosts which revealed perturbation in the levels of some PrLP-encoding genes during interactions with plants. Overall, our work sheds light into the probable role of prion-like candidates in plant-fungi interaction, particularly in context of pathogenesis, paving way for more focused studies for validating their role.
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Affiliation(s)
- Sampurna Garai
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Avi Raizada
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India
| | - Vijay Kumar
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India
| | - Sudhir K Sopory
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Ashwani Pareek
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Charanpreet Kaur
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
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17
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Workman RJ, Huang CJ, Lynch GC, Pettitt BM. Peptide diffusion in biomolecular condensates. Biophys J 2024; 123:1668-1675. [PMID: 38751116 PMCID: PMC11213990 DOI: 10.1016/j.bpj.2024.05.009] [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: 11/29/2023] [Revised: 04/22/2024] [Accepted: 05/10/2024] [Indexed: 05/30/2024] Open
Abstract
Diffusion determines the turnover of biomolecules in liquid-liquid phase-separated condensates. We considered the mean square displacement and thus the diffusion constant for simple model systems of peptides GGGGG, GGQGG, and GGVGG in aqueous solutions after phase separation by simulating atomic-level models. These solutions readily separate into aqueous and peptide-rich droplet phases. We noted the effect of the peptides being in a solvated, surface, or droplet state on the peptide's diffusion coefficients. Both sequence and peptide conformational distribution were found to influence diffusion and condensate turnover in these systems, with sequence dominating the magnitude of the differences. We found that the most compact structures for each sequence diffused the fastest in the peptide-rich condensate phase. This model result may have implications for turnover dynamics in signaling systems.
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Affiliation(s)
- Riley J Workman
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas
| | - Caleb J Huang
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas
| | - Gillian C Lynch
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas
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18
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Di Timoteo G, Giuliani A, Setti A, Biagi MC, Lisi M, Santini T, Grandioso A, Mariani D, Castagnetti F, Perego E, Zappone S, Lattante S, Sabatelli M, Rotili D, Vicidomini G, Bozzoni I. M 6A reduction relieves FUS-associated ALS granules. Nat Commun 2024; 15:5033. [PMID: 38866783 PMCID: PMC11169559 DOI: 10.1038/s41467-024-49416-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease due to gradual motoneurons (MN) degeneration. Among the processes associated to ALS pathogenesis, there is the formation of cytoplasmic inclusions produced by aggregation of mutant proteins, among which the RNA binding protein FUS. Here we show that, in neuronal cells and in iPSC-derived MN expressing mutant FUS, such inclusions are significantly reduced in number and dissolve faster when the RNA m6A content is diminished. Interestingly, stress granules formed in ALS conditions showed a distinctive transcriptome with respect to control cells, which reverted to similar to control after m6A downregulation. Notably, cells expressing mutant FUS were characterized by higher m6A levels suggesting a possible link between m6A homeostasis and pathological aggregates. Finally, we show that FUS inclusions are reduced also in patient-derived fibroblasts treated with STM-2457, an inhibitor of METTL3 activity, paving the way for its possible use for counteracting aggregate formation in ALS.
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Grants
- ERC-2019-SyG 855923-ASTRA EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- ERC-2018-CoG 818669-BrightEyes EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- AIRC IG 2019 Id. 23053 Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)
- PRIN 2017 2017P352Z4 Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- NextGenerationEU PNRR MUR Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- "National Center for Gene Therapy and Drugbased on RNA Technology" (CN00000041) Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- "National Center for Gene Therapy and Drug based on RNA Technology" (CN00000041) Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- NextGenerationEU PNRR MUR Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- "Sapienza" Ateneo Project 2021 n. RM12117A61C811CE Sapienza Università di Roma (Sapienza University of Rome)
- Regione Lazio PROGETTI DI GRUPPI DI RICERCA 2020 - A0375-2020-36597 Regione Lazio (Region of Lazio)
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Affiliation(s)
- Gaia Di Timoteo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Andrea Giuliani
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Adriano Setti
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Martina C Biagi
- Center for Life Nano- & Neuro-Science@Sapienza, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, 00161, Italy
| | - Michela Lisi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Alessia Grandioso
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Davide Mariani
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Francesco Castagnetti
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Eleonora Perego
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Sabrina Zappone
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Serena Lattante
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Mario Sabatelli
- Section of Neurology, Department of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Adult NEMO Clinical Center, Unit of Neurology, Department of Aging, Neurological, Orthopedic and Head-Neck Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Giuseppe Vicidomini
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy.
- Center for Life Nano- & Neuro-Science@Sapienza, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, 00161, Italy.
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy.
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19
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Wu X, Zhang L, Liu C, Cheng Q, Zhao W, Chen P, Qin Y, Chen M. The NS2B-PP1α-eIF2α axis: Inhibiting stress granule formation and Boosting Zika virus replication. PLoS Pathog 2024; 20:e1012355. [PMID: 38935808 PMCID: PMC11236161 DOI: 10.1371/journal.ppat.1012355] [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: 12/08/2023] [Revised: 07/10/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024] Open
Abstract
Stress granules (SGs), formed by untranslated messenger ribonucleoproteins (mRNPs) during cellular stress in eukaryotes, have been linked to flavivirus interference without clear understanding. This study reveals the role of Zika virus (ZIKV) NS2B as a scaffold protein mediating interaction between protein phosphatase 1α (PP1α) and eukaryotic initiation factor 2α (eIF2α). This interaction promotes eIF2α dephosphorylation by PP1α, inhibiting SG formation. The NS2B-PP1α complex exhibits remarkable stability, resisting ubiquitin-induced degradation and amplifying eIF2α dephosphorylation, thus promoting ZIKV replication. In contrast, the NS2BV35A mutant, interacting exclusively with eIF2α, fails to inhibit SG formation, resulting in reduced viral replication and diminished impact on brain organoid growth. These findings reveal PP1α's dual role in ZIKV infection, inducing interferon production as an antiviral factor and suppressing SG formation as a viral promoter. Moreover, we found that NS2B also serves as a versatile mechanism employed by flaviviruses to counter host antiviral defenses, primarily by broadly inhibiting SG formation. This research advances our comprehension of the complex interplay in flavivirus-host interactions, offering potential for innovative therapeutic strategies against flavivirus infections.
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Affiliation(s)
- Xiaoyan Wu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Linliang Zhang
- College of Life Sciences, Hubei University, Wuhan, China
| | - Cong Liu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qi Cheng
- Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Wen Zhao
- Tissue Engineering and Organ Manufacturing (TEOM) lab, Department of Biomedical Engineering, Wuhan University Taikang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Pu Chen
- Tissue Engineering and Organ Manufacturing (TEOM) lab, Department of Biomedical Engineering, Wuhan University Taikang Medical School (School of Basic Medical Sciences), Wuhan, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
- College of Life Sciences, Hubei University, Wuhan, China
| | - Mingzhou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
- College of Life Sciences, Hubei University, Wuhan, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
- Hubei Jiangxia Laboratory, Wuhan, China
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20
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Kwon E, Jung DM, Kim EM, Kim KK. A new G3BP1-GFP reporter system for assessing skin toxicity by real-time monitoring of stress granules in vitro. Toxicol Lett 2024; 397:48-54. [PMID: 38734221 DOI: 10.1016/j.toxlet.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Abstract
The skin, the organ with the largest surface area in the body, is the most susceptible to chemical exposure from the external environment. In this study, we aimed to establish an in vitro skin toxicity monitoring system that utilizes the mechanism of stress granule (SG) formation induced by various cellular stresses. In HaCaT cells, a keratinocyte cell line that comprises the human skin, a green fluorescent protein (GFP) was knocked in at the C-terminal genomic locus of Ras GTPase-activating protein-binding protein 1 (G3BP1), a representative component of SGs. The G3BP1-GFP knock-in HaCaT cells and wild-type (WT) HaCaT cells formed SGs containing G3BP1-GFP upon exposure to arsenite and household chemicals, such as bisphenol A (BPA) and benzalkonium chloride (BAC), in real-time. In addition, the exposure of G3BP1-GFP knock-in HaCaT cells to BPA and BAC promoted the phosphorylation of eukaryotic initiation factor 2 alpha and protein kinase R-like endoplasmic reticulum kinase, which are cell signaling factors involved in SG formation, similar to WT HaCaT cells. In conclusion, this novel G3BP1-GFP knock-in human skin cell system can monitor SG formation in real-time and be utilized to assess skin toxicity to various substances.
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Affiliation(s)
- Eunhye Kwon
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Da-Min Jung
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Eun-Mi Kim
- Department of Bio and Environmental Technology, College of Science and Convergence Technology, Seoul Women's University, Seoul 01797, Republic of Korea.
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, Republic of Korea.
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21
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Buchan JR. Stress granule and P-body clearance: Seeking coherence in acts of disappearance. Semin Cell Dev Biol 2024; 159-160:10-26. [PMID: 38278052 PMCID: PMC10939798 DOI: 10.1016/j.semcdb.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/28/2024]
Abstract
Stress granules and P-bodies are conserved cytoplasmic biomolecular condensates whose assembly and composition are well documented, but whose clearance mechanisms remain controversial or poorly described. Such understanding could provide new insight into how cells regulate biomolecular condensate formation and function, and identify therapeutic strategies in disease states where aberrant persistence of stress granules in particular is implicated. Here, I review and compare the contributions of chaperones, the cytoskeleton, post-translational modifications, RNA helicases, granulophagy and the proteasome to stress granule and P-body clearance. Additionally, I highlight the potentially vital role of RNA regulation, cellular energy, and changes in the interaction networks of stress granules and P-bodies as means of eliciting clearance. Finally, I discuss evidence for interplay of distinct clearance mechanisms, suggest future experimental directions, and suggest a simple working model of stress granule clearance.
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Affiliation(s)
- J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson 85716, United States.
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22
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Huang M, Liu YU, Yao X, Qin D, Su H. Variability in SOD1-associated amyotrophic lateral sclerosis: geographic patterns, clinical heterogeneity, molecular alterations, and therapeutic implications. Transl Neurodegener 2024; 13:28. [PMID: 38811997 PMCID: PMC11138100 DOI: 10.1186/s40035-024-00416-x] [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: 01/29/2024] [Accepted: 04/17/2024] [Indexed: 05/31/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive loss of motor neurons, resulting in global health burden and limited post-diagnosis life expectancy. Although primarily sporadic, familial ALS (fALS) cases suggest a genetic basis. This review focuses on SOD1, the first gene found to be associated with fALS, which has been more recently confirmed by genome sequencing. While informative, databases such as ALSoD and STRENGTH exhibit regional biases. Through a systematic global examination of SOD1 mutations from 1993 to 2023, we found different geographic distributions and clinical presentations. Even though different SOD1 variants are expressed at different protein levels and have different half-lives and dismutase activities, these alterations lead to loss of function that is not consistently correlated with disease severity. Gain of function of toxic aggregates of SOD1 resulting from mutated SOD1 has emerged as one of the key contributors to ALS. Therapeutic interventions specifically targeting toxic gain of function of mutant SOD1, including RNA interference and antibodies, show promise, but a cure remains elusive. This review provides a comprehensive perspective on SOD1-associated ALS and describes molecular features and the complex genetic landscape of SOD1, highlighting its importance in determining diverse clinical manifestations observed in ALS patients and emphasizing the need for personalized therapeutic strategies.
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Affiliation(s)
- Miaodan Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Macao, China
| | - Yong U Liu
- Laboratory for Neuroimmunology in Health and Diseases, Guangzhou First People's Hospital School of Medicine, South China University of Technology, Guangzhou, China
| | - Xiaoli Yao
- Department of Neurology, The First Affiliated Hospital, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China.
| | - Dajiang Qin
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510799, China.
| | - Huanxing Su
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Macao, China.
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23
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Yan X, Kuster D, Mohanty P, Nijssen J, Pombo-García K, Rizuan A, Franzmann TM, Sergeeva A, Passos PM, George L, Wang SH, Shenoy J, Danielson HL, Honigmann A, Ayala YM, Fawzi NL, Mittal J, Alberti S, Hyman AA. Intra-condensate demixing of TDP-43 inside stress granules generates pathological aggregates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576837. [PMID: 38328053 PMCID: PMC10849624 DOI: 10.1101/2024.01.23.576837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Cytosolic aggregation of the nuclear protein TDP-43 is associated with many neurodegenerative diseases, but the triggers for TDP-43 aggregation are still debated. Here, we demonstrate that TDP-43 aggregation requires a double event. One is up-concentration in stress granules beyond a threshold, and the other is oxidative stress. These two events collectively induce intra-condensate demixing, giving rise to a dynamic TDP-43 enriched phase within stress granules, which subsequently transitions into pathological aggregates. Mechanistically, intra-condensate demixing is triggered by local unfolding of the RRM1 domain for intermolecular disulfide bond formation and by increased hydrophobic patch interactions in the C-terminal domain. By engineering TDP-43 variants resistant to intra-condensate demixing, we successfully eliminate pathological TDP-43 aggregates in cells. We conclude that up-concentration inside condensates and simultaneous exposure to environmental stress could be a general pathway for protein aggregation, with intra-condensate demixing constituting a key intermediate step.
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Affiliation(s)
- Xiao Yan
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
| | - David Kuster
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- These authors contributed equally
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University; College Station, TX 77843; USA
- These authors contributed equally
| | - Jik Nijssen
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- These authors contributed equally
| | - Karina Pombo-García
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- These authors contributed equally
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University; College Station, TX 77843; USA
| | - Titus M. Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden; Dresden, Saxony, 01307; Germany
| | - Aleksandra Sergeeva
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden; Dresden, Saxony, 01307; Germany
| | - Patricia M. Passos
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University; St. Louis, MO 63104; USA
| | - Leah George
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University; St. Louis, MO 63104; USA
| | - Szu-Huan Wang
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University; Providence, RI 02912; USA
| | - Jayakrishna Shenoy
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University; Providence, RI 02912; USA
| | - Helen L. Danielson
- Center for Biomedical Engineering, Brown University; Providence, RI 02912; USA
| | - Alf Honigmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden; Dresden, Saxony, 01307; Germany
| | - Yuna M. Ayala
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University; St. Louis, MO 63104; USA
| | - Nicolas L. Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University; Providence, RI 02912; USA
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University; College Station, TX 77843; USA
- Department of Chemistry, Texas A&M University; College Station, TX 77843; USA
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University; College Station, TX 77843; USA
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden; Dresden, Saxony, 01307; Germany
| | - Anthony A. Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- Lead contact
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24
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Shelkovnikova TA, Hautbergue GM. RNP granules in ALS and neurodegeneration: From multifunctional membraneless organelles to therapeutic opportunities. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2024; 176:455-479. [PMID: 38802180 DOI: 10.1016/bs.irn.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) and related neurodegenerative diseases are characterised by dysfunction of a host of RNA-binding proteins (RBPs) and a severely disrupted RNA metabolism. Recently, RBP-harbouring phase-separated complexes, ribonucleoprotein (RNP) granules, have come into the limelight as "crucibles" of neuronal pathology in ALS. RNP granules are indispensable for the multitude of regulatory processes underlying cellular RNA metabolism and serve as critical organisers of cellular biochemistry. Neurons, highly specialised cells, heavily rely on RNP granules for efficient trafficking, signalling and stress responses. Multiple RNP granule components, primarily RBPs such as TDP-43 and FUS, are affected by ALS mutations. However, even in the absence of mutations, RBP proteinopathies represent pathophysiological hallmarks of ALS. Given the high local concentrations of RBPs and RNAs, their weakened or enhanced interactions within RNP granules disrupt their homeostasis. Thus, the physiological process of phase separation and RNP granule formation, vital for maintaining the high-functioning state of neuronal cells, becomes their Achilles heel. Here, we will review the recent literature on the causes and consequences of abnormal RNP granule functioning in ALS and related disorders. In particular, we will summarise the evidence for the network-level dysfunction of RNP granules in these conditions and discuss considerations for therapeutic interventions to target RBPs, RNP granules and their network as a whole.
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Affiliation(s)
- Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom.
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom; Healthy Lifespan Institute (HELSI), University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom.
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25
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Mann N, Hill J, Wang K, Hughes RM. OptoProfilin: A Single Component Biosensor of Applied Cellular Stress. Chembiochem 2024; 25:e202400007. [PMID: 38457348 PMCID: PMC11218921 DOI: 10.1002/cbic.202400007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
The actin cytoskeleton is a biosensor of cellular stress and a potential prognosticator of human disease. In particular, aberrant cytoskeletal structures such as stress granules formed in response to energetic and oxidative stress are closely linked to ageing, cancer, cardiovascular disease, and viral infection. Whether these cytoskeletal phenomena can be harnessed for the development of biosensors for cytoskeletal dysfunction and, by extension, disease progression, remains an open question. In this work, we describe the design and development of an optogenetic iteration of profilin, an actin monomer binding protein with critical functions in cytoskeletal dynamics. We demonstrate that this optically activated profilin ('OptoProfilin') can act as an optically triggered biosensor of applied cellular stress in select immortalized cell lines. Notably, OptoProfilin is a single component biosensor, likely increasing its utility for experimentalists. While a large body of preexisting work closely links profilin activity with cellular stress and neurodegenerative disease, this, to our knowledge, is the first example of profilin as an optogenetic biosensor of stress-induced changes in the cytoskeleton.
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Affiliation(s)
- Noah Mann
- Department of Chemistry, East Carolina University, Greenville, North Carolina, United States
| | - Jahiem Hill
- Department of Chemistry, East Carolina University, Greenville, North Carolina, United States
| | - Kenneth Wang
- Department of Chemistry, Davidson College, Davidson, North Carolina, United States
| | - Robert M Hughes
- Department of Chemistry, East Carolina University, Greenville, North Carolina, United States
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26
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Petrauskas A, Fortunati DL, Kandi AR, Pothapragada SS, Agrawal K, Singh A, Huelsmeier J, Hillebrand J, Brown G, Chaturvedi D, Lee J, Lim C, Auburger G, VijayRaghavan K, Ramaswami M, Bakthavachalu B. Structured and disordered regions of Ataxin-2 contribute differently to the specificity and efficiency of mRNP granule formation. PLoS Genet 2024; 20:e1011251. [PMID: 38768217 PMCID: PMC11166328 DOI: 10.1371/journal.pgen.1011251] [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: 01/27/2024] [Revised: 06/11/2024] [Accepted: 04/05/2024] [Indexed: 05/22/2024] Open
Abstract
Ataxin-2 (ATXN2) is a gene implicated in spinocerebellar ataxia type II (SCA2), amyotrophic lateral sclerosis (ALS) and Parkinsonism. The encoded protein is a therapeutic target for ALS and related conditions. ATXN2 (or Atx2 in insects) can function in translational activation, translational repression, mRNA stability and in the assembly of mRNP-granules, a process mediated by intrinsically disordered regions (IDRs). Previous work has shown that the LSm (Like-Sm) domain of Atx2, which can help stimulate mRNA translation, antagonizes mRNP-granule assembly. Here we advance these findings through a series of experiments on Drosophila and human Ataxin-2 proteins. Results of Targets of RNA Binding Proteins Identified by Editing (TRIBE), co-localization and immunoprecipitation experiments indicate that a polyA-binding protein (PABP) interacting, PAM2 motif of Ataxin-2 may be a major determinant of the mRNA and protein content of Ataxin-2 mRNP granules. Experiments with transgenic Drosophila indicate that while the Atx2-LSm domain may protect against neurodegeneration, structured PAM2- and unstructured IDR- interactions both support Atx2-induced cytotoxicity. Taken together, the data lead to a proposal for how Ataxin-2 interactions are remodelled during translational control and how structured and non-structured interactions contribute differently to the specificity and efficiency of RNP granule condensation as well as to neurodegeneration.
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Affiliation(s)
- Arnas Petrauskas
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Daniel L. Fortunati
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Arvind Reddy Kandi
- School of Biosciences and Bioengineering, Indian Institute of Technology, Mandi, India
| | | | - Khushboo Agrawal
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore, India
- School of Biotechnology, Amrita Vishwa Vidyapeetham University, Kollam, Kerala, India
| | - Amanjot Singh
- National Centre for Biological Sciences, TIFR, Bangalore, India
- Manipal Institute of Regenerative Medicine, MAHE-Bengaluru, Govindapura, Bengaluru, India
| | - Joern Huelsmeier
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Jens Hillebrand
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Georgia Brown
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | | | - Jongbo Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, Republic of Korea
| | - Chunghun Lim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, Republic of Korea
| | - Georg Auburger
- Experimental Neurology, Medical School, Goethe University, Frankfurt, Germany
| | | | - Mani Ramaswami
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Baskar Bakthavachalu
- School of Biosciences and Bioengineering, Indian Institute of Technology, Mandi, India
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore, India
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27
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Swindell WR. Meta-analysis of differential gene expression in lower motor neurons isolated by laser capture microdissection from post-mortem ALS spinal cords. Front Genet 2024; 15:1385114. [PMID: 38689650 PMCID: PMC11059082 DOI: 10.3389/fgene.2024.1385114] [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: 02/11/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction ALS is a fatal neurodegenerative disease for which underlying mechanisms are incompletely understood. The motor neuron is a central player in ALS pathogenesis but different transcriptome signatures have been derived from bulk analysis of post-mortem tissue and iPSC-derived motor neurons (iPSC-MNs). Methods This study performed a meta-analysis of six gene expression studies (microarray and RNA-seq) in which laser capture microdissection (LCM) was used to isolate lower motor neurons from post-mortem spinal cords of ALS and control (CTL) subjects. Differentially expressed genes (DEGs) with consistent ALS versus CTL expression differences across studies were identified. Results The analysis identified 222 ALS-increased DEGs (FDR <0.10, SMD >0.80) and 278 ALS-decreased DEGs (FDR <0.10, SMD < -0.80). ALS-increased DEGs were linked to PI3K-AKT signaling, innate immunity, inflammation, motor neuron differentiation and extracellular matrix. ALS-decreased DEGs were associated with the ubiquitin-proteosome system, microtubules, axon growth, RNA-binding proteins and synaptic membrane. ALS-decreased DEG mRNAs frequently interacted with RNA-binding proteins (e.g., FUS, HuR). The complete set of DEGs (increased and decreased) overlapped significantly with genes near ALS-associated SNP loci (p < 0.01). Transcription factor target motifs with increased proximity to ALS-increased DEGs were identified, most notably DNA elements predicted to interact with forkhead transcription factors (e.g., FOXP1) and motor neuron and pancreas homeobox 1 (MNX1). Some of these DNA elements overlie ALS-associated SNPs within known enhancers and are predicted to have genotype-dependent MNX1 interactions. DEGs were compared to those identified from SOD1-G93A mice and bulk spinal cord segments or iPSC-MNs from ALS patients. There was good correspondence with transcriptome changes from SOD1-G93A mice (r ≤ 0.408) but most DEGs were not differentially expressed in bulk spinal cords or iPSC-MNs and transcriptome-wide effect size correlations were weak (bulk tissue: r ≤ 0.207, iPSC-MN: r ≤ 0.037). Conclusion This study defines a robust transcriptome signature from LCM-based motor neuron studies of post-mortem tissue from ALS and CTL subjects. This signature differs from those obtained from analysis of bulk spinal cord segments and iPSC-MNs. Results provide insight into mechanisms underlying gene dysregulation in ALS and highlight connections between these mechanisms, ALS genetics, and motor neuron biology.
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Affiliation(s)
- William R. Swindell
- Department of Internal Medicine, Division of Hospital Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
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28
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Khorsand FR, Uversky VN. Liquid-liquid phase separation as triggering factor of fibril formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:143-182. [PMID: 38811080 DOI: 10.1016/bs.pmbts.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Liquid-liquid phase separation (LLPS) refers to the phenomenon, where a homogeneous solution spontaneously undergoes a transition into two or more immiscible phases. Through transient weak multivalent macromolecular interactions, a homogeneous solution can spontaneously separate into two phases: one rich in biomolecules and the other poor in biomolecules. Phase separation is believed to serve as the physicochemical foundation for the formation of membrane-less organelles (MLOs) and bio-molecular condensates within cells. Moreover, numerous biological processes depend on LLPS, such as transcription, immunological response, chromatin architecture, DNA damage response, stress granule formation, viral infection, etc. Abnormalities in phase separation can lead to diseases, such as cancer, neurodegeneration, and metabolic disorders. LLPS is regulated by various factors, such as concentration of molecules undergoing LLPS, salt concentration, pH, temperature, post-translational modifications, and molecular chaperones. Recent research on LLPS of biomolecules has progressed rapidly and led to the development of databases containing information pertaining to various aspects of the biomolecule separation analysis. However, more comprehensive research is still required to fully comprehend the specific molecular mechanisms and biological effects of LLPS.
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Affiliation(s)
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Moscow, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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29
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Liang P, Wu Y, Zheng S, Zhang J, Yang S, Wang J, Ma S, Zhang M, Gu Z, Liu Q, Jiang W, Xing Q, Wang B. Paxillin phase separation promotes focal adhesion assembly and integrin signaling. J Cell Biol 2024; 223:e202209027. [PMID: 38466167 PMCID: PMC10926639 DOI: 10.1083/jcb.202209027] [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: 09/08/2022] [Revised: 12/04/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2024] Open
Abstract
Focal adhesions (FAs) are transmembrane protein assemblies mediating cell-matrix connection. Although protein liquid-liquid phase separation (LLPS) has been tied to the organization and dynamics of FAs, the underlying mechanisms remain unclear. Here, we experimentally tune the LLPS of PXN/Paxillin, an essential scaffold protein of FAs, by utilizing a light-inducible Cry2 system in different cell types. In addition to nucleating FA components, light-triggered PXN LLPS potently activates integrin signaling and subsequently accelerates cell spreading. In contrast to the homotypic interaction-driven LLPS of PXN in vitro, PXN condensates in cells are associated with the plasma membrane and modulated by actomyosin contraction and client proteins of FAs. Interestingly, non-specific weak intermolecular interactions synergize with specific molecular interactions to mediate the multicomponent condensation of PXN and are efficient in promoting FA assembly and integrin signaling. Thus, our data establish an active role of the PXN phase transition into a condensed membrane-associated compartment in promoting the assembly/maturation of FAs.
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Affiliation(s)
- Peigang Liang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuchen Wu
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shanyuan Zheng
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiaqi Zhang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shuo Yang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jinfang Wang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Suibin Ma
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mengjun Zhang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zhuang Gu
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qingfeng Liu
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Wenxue Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Qiong Xing
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Bo Wang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
- Shenzhen Research Institute of Xiamen University, Shenzhen, China
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30
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Barrow ER, Valionyte E, Baxter CR, Yang Y, Herath S, O'Connell WA, Lopatecka J, Strachan A, Woznica W, Stephenson HN, Fejer G, Sharma V, Lu B, Luo S. Discovery of SQSTM1/p62-dependent P-bodies that regulate the NLRP3 inflammasome. Cell Rep 2024; 43:113935. [PMID: 38460129 DOI: 10.1016/j.celrep.2024.113935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/22/2024] [Accepted: 02/22/2024] [Indexed: 03/11/2024] Open
Abstract
Autophagy and ribonucleoprotein granules, such as P-bodies (PBs) and stress granules, represent vital stress responses to maintain cellular homeostasis. SQSTM1/p62 phase-separated droplets are known to play critical roles in selective autophagy; however, it is unknown whether p62 can exist as another form in addition to its autophagic droplets. Here, we found that, under stress conditions, including proteotoxicity, endotoxicity, and oxidation, autophagic p62 droplets are transformed to a type of enlarged PBs, termed p62-dependent P-bodies (pd-PBs). p62 phase separation is essential for the nucleation of pd-PBs. Mechanistically, pd-PBs are triggered by enhanced p62 droplet formation upon stress stimulation through the interactions between p62 and DDX6, a DEAD-box ATPase. Functionally, pd-PBs recruit the NLRP3 inflammasome adaptor ASC to assemble the NLRP3 inflammasome and induce inflammation-associated cytotoxicity. Our study shows that p62 droplet-to-PB transformation acts as a stress response to activate the NLRP3 inflammasome process, suggesting that persistent pd-PBs lead to NLRP3-dependent inflammation toxicity.
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Affiliation(s)
- Elizabeth R Barrow
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Evelina Valionyte
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Chris R Baxter
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Yi Yang
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Sharon Herath
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - William A O'Connell
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Justyna Lopatecka
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Drake Circus, PL4 8AA Plymouth, UK
| | - Alexander Strachan
- Plymouth Electron Microscopy Centre, University of Plymouth, Drake Circus, PL4 8AA Plymouth, UK
| | - Waldemar Woznica
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Holly N Stephenson
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Gyorgy Fejer
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Drake Circus, PL4 8AA Plymouth, UK
| | - Vikram Sharma
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Drake Circus, PL4 8AA Plymouth, UK
| | - Boxun Lu
- State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Shouqing Luo
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK.
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31
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Nomura S, Miyasaka A, Maruyama A, Shimada N. Spontaneous Liquid Droplet-to-Gel Transition of Citrulline Polypeptide Complexed with Nucleic Acids. ACS Biomater Sci Eng 2024; 10:1473-1480. [PMID: 38404112 DOI: 10.1021/acsbiomaterials.3c01716] [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: 02/27/2024]
Abstract
Inside cells, proteins complex with nucleic acids to form liquid droplets resulting from liquid-liquid phase separation. The presence of mutated proteins can change the state of these liquid droplets to solids or gels, triggering neurodegenerative diseases. The mechanism of the liquid to solid or gel transition is still unclear. Solutions of poly(l-ornithine-co-l-citrulline) (PLOC) copolymers, which exhibit upper critical solution temperature-type behavior, change state upon cooling. In this study, we evaluated the effect of nucleic acids complexed with PLOC on phase changes. In the presence of nucleic acids, such as polyC and polyU, PLOC formed liquid droplets at low temperatures. The droplets dissolved at temperatures above the phase separation temperature. The phase separation temperature depended on the chemical structure of the nucleobase, implying that electrostatic and hydrogen bonding interactions between the nucleic acid and PLOC influenced phase separation. Furthermore, the liquid droplets spontaneously changed to gel-like precipitates due to spontaneous release of nucleic acids from the complex. The rate of the liquid droplet-to-gel transition depended on the magnitude of electrostatic and hydrogen bonding interactions between PLOC and nucleic acid. PLOC complexed with mRNA also underwent a liquid droplet-to-gel transition upon the release of mRNA. This work provides insights into the mechanism of pathogenic transitions of the cellular droplets.
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Affiliation(s)
- Shouhei Nomura
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Ayano Miyasaka
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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32
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Das T, Zaidi F, Farag M, Ruff KM, Messing J, Taylor JP, Pappu RV, Mittag T. Metastable condensates suppress conversion to amyloid fibrils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582569. [PMID: 38464104 PMCID: PMC10925303 DOI: 10.1101/2024.02.28.582569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Stress granules form via co-condensation of RNA binding proteins with prion-like low complexity domains (PLCDs) and RNA molecules released by stress-induced polysomal runoff. Homotypic interactions among PLCDs can drive amyloid fibril formation and this is enhanced by ALS-associated mutations. We find that homotypic interactions that drive condensation versus fibril formation are separable for A1-LCD, the PLCD of hnRNPA1. These separable interactions lead to condensates that are metastable versus fibrils that are globally stable. Metastable condensates suppress fibril formation, and ALS-associated mutations enhance fibril formation by weakening condensate metastability. Mutations designed to enhance A1-LCD condensate metastability restore wild-type behaviors of stress granules in cells even when ALS-associated mutations are present. This suggests that fibril formation can be suppressed by enhancing condensate metastability through condensate-driving interactions.
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Affiliation(s)
- Tapojyoti Das
- Department of Structural Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Fatima Zaidi
- Department of Structural Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Mina Farag
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - James Messing
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - J. Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
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Demongin C, Tranier S, Joshi V, Ceschi L, Desforges B, Pastré D, Hamon L. RNA and the RNA-binding protein FUS act in concert to prevent TDP-43 spatial segregation. J Biol Chem 2024; 300:105716. [PMID: 38311174 PMCID: PMC10912363 DOI: 10.1016/j.jbc.2024.105716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/10/2024] Open
Abstract
FUS and TDP-43 are two self-adhesive aggregation-prone mRNA-binding proteins whose pathological mutations have been linked to neurodegeneration. While TDP-43 and FUS form reversible mRNA-rich compartments in the nucleus, pathological mutations promote their respective cytoplasmic aggregation in neurons with no apparent link between the two proteins except their intertwined function in mRNA processing. By combining analyses in cellular context and at high resolution in vitro, we unraveled that TDP-43 is specifically recruited in FUS assemblies to form TDP-43-rich subcompartments but without reciprocity. The presence of mRNA provides an additional scaffold to promote the mixing between TDP-43 and FUS. Accordingly, we also found that the pathological truncated form of TDP-43, TDP-25, which has an impaired RNA-binding ability, no longer mixes with FUS. Together, these results suggest that the binding of FUS along nascent mRNAs enables TDP-43, which is highly aggregation-prone, to mix with FUS phase to form mRNA-rich subcompartments. A functional link between FUS and TDP-43 may explain their common implication in amyotrophic lateral sclerosis.
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Affiliation(s)
- Clément Demongin
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | - Samuel Tranier
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Vandana Joshi
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | - Léa Ceschi
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | | | - David Pastré
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | - Loic Hamon
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France.
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Wang X, Fan X, Zhang J, Wang F, Chen J, Wen Y, Wang L, Li T, Li H, Gu H, Zhang Y, Yuan S. hnRNPA2B1 represses the disassembly of arsenite-induced stress granules and is essential for male fertility. Cell Rep 2024; 43:113769. [PMID: 38363675 DOI: 10.1016/j.celrep.2024.113769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/19/2023] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
Although the composition and assembly of stress granules (SGs) are well understood, the molecular mechanisms underlying SG disassembly remain unclear. Here, we identify that heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2B1) is associated with SGs and that its absence specifically enhances the disassembly of arsenite-induced SGs depending on the ubiquitination-proteasome system but not the autophagy pathway. hnRNPA2B1 interacts with many core SG proteins, including G3BP1, G3BP2, USP10, and Caprin-1; USP10 can deubiquitinate G3BP1; and hnRNPA2B1 depletion attenuates the G3BP1-USP10/Caprin-1 interaction but elevates the G3BP1 ubiquitination level under arsenite treatment. Moreover, the disease-causing mutation FUSR521C also disassembles faster from SGs in HNRNPA2B1 mutant cells. Furthermore, knockout of hnRNPA2B1 in mice leads to Sertoli cell-only syndrome (SCOS), causing complete male infertility. Consistent with this, arsenite-induced SGs disassemble faster in Hnrnpa2b1 knockout (KO) mouse Sertoli cells as well. These findings reveal the essential roles of hnRNPA2B1 in regulating SG disassembly and male mouse fertility.
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Affiliation(s)
- Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Xu Fan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jin Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Fengli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jingshou Chen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yujiao Wen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lingjuan Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tao Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Huaibiao Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Heng Gu
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou 510600, China
| | - Youzhi Zhang
- School of Pharmacy, Hubei University of Science and Technology, Xianning 437100, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Laboratory of the Animal Center, Huazhong University of Science and Technology, Wuhan 430030, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518057, China.
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35
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Pernin F, Cui QL, Mohammadnia A, Fernandes MGF, Hall JA, Srour M, Dudley RWR, Zandee SEJ, Klement W, Prat A, Salapa HE, Levin MC, Moore GRW, Kennedy TE, Vande Velde C, Antel JP. Regulation of stress granule formation in human oligodendrocytes. Nat Commun 2024; 15:1524. [PMID: 38374028 PMCID: PMC10876533 DOI: 10.1038/s41467-024-45746-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Oligodendrocyte (OL) injury and subsequent loss is a pathologic hallmark of multiple sclerosis (MS). Stress granules (SGs) are membrane-less organelles containing mRNAs stalled in translation and considered as participants of the cellular response to stress. Here we show SGs in OLs in active and inactive areas of MS lesions as well as in normal-appearing white matter. In cultures of primary human adult brain derived OLs, metabolic stress conditions induce transient SG formation in these cells. Combining pro-inflammatory cytokines, which alone do not induce SG formation, with metabolic stress results in persistence of SGs. Unlike sodium arsenite, metabolic stress induced SG formation is not blocked by the integrated stress response inhibitor. Glycolytic inhibition also induces persistent SGs indicating the dependence of SG formation and disassembly on the energetic glycolytic properties of human OLs. We conclude that SG persistence in OLs in MS reflects their response to a combination of metabolic stress and pro-inflammatory conditions.
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Affiliation(s)
- Florian Pernin
- Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Qiao-Ling Cui
- Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | | | - Milton G F Fernandes
- Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Jeffery A Hall
- Department of Neurosurgery, McGill University Health Centre, Montreal, QC, Canada
| | - Myriam Srour
- Division of Pediatric Neurology, Montreal Children's Hospital, Montreal, QC, Canada
| | - Roy W R Dudley
- Department of Pediatric Neurosurgery, Montreal Children's Hospital, Montreal, QC, Canada
| | - Stephanie E J Zandee
- Centre de Recherche Hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Wendy Klement
- Centre de Recherche Hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Alexandre Prat
- Centre de Recherche Hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Hannah E Salapa
- Cameco Multiple Sclerosis Neuroscience Research Center, University of Saskatchewan, Saskatoon, SK, Canada
| | - Michael C Levin
- Cameco Multiple Sclerosis Neuroscience Research Center, University of Saskatchewan, Saskatoon, SK, Canada
| | - G R Wayne Moore
- Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Timothy E Kennedy
- Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | | | - Jack P Antel
- Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, QC, Canada.
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36
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Firdaus Z, Li X. Unraveling the Genetic Landscape of Neurological Disorders: Insights into Pathogenesis, Techniques for Variant Identification, and Therapeutic Approaches. Int J Mol Sci 2024; 25:2320. [PMID: 38396996 PMCID: PMC10889342 DOI: 10.3390/ijms25042320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Genetic abnormalities play a crucial role in the development of neurodegenerative disorders (NDDs). Genetic exploration has indeed contributed to unraveling the molecular complexities responsible for the etiology and progression of various NDDs. The intricate nature of rare and common variants in NDDs contributes to a limited understanding of the genetic risk factors associated with them. Advancements in next-generation sequencing have made whole-genome sequencing and whole-exome sequencing possible, allowing the identification of rare variants with substantial effects, and improving the understanding of both Mendelian and complex neurological conditions. The resurgence of gene therapy holds the promise of targeting the etiology of diseases and ensuring a sustained correction. This approach is particularly enticing for neurodegenerative diseases, where traditional pharmacological methods have fallen short. In the context of our exploration of the genetic epidemiology of the three most prevalent NDDs-amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease, our primary goal is to underscore the progress made in the development of next-generation sequencing. This progress aims to enhance our understanding of the disease mechanisms and explore gene-based therapies for NDDs. Throughout this review, we focus on genetic variations, methodologies for their identification, the associated pathophysiology, and the promising potential of gene therapy. Ultimately, our objective is to provide a comprehensive and forward-looking perspective on the emerging research arena of NDDs.
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Affiliation(s)
- Zeba Firdaus
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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37
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Ueda T, Takeuchi T, Fujikake N, Suzuki M, Minakawa EN, Ueyama M, Fujino Y, Kimura N, Nagano S, Yokoseki A, Onodera O, Mochizuki H, Mizuno T, Wada K, Nagai Y. Dysregulation of stress granule dynamics by DCTN1 deficiency exacerbates TDP-43 pathology in Drosophila models of ALS/FTD. Acta Neuropathol Commun 2024; 12:20. [PMID: 38311779 PMCID: PMC10840176 DOI: 10.1186/s40478-024-01729-8] [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: 09/01/2023] [Accepted: 01/11/2024] [Indexed: 02/06/2024] Open
Abstract
The abnormal aggregation of TDP-43 into cytoplasmic inclusions in affected neurons is a major pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Although TDP-43 is aberrantly accumulated in the neurons of most patients with sporadic ALS/FTD and other TDP-43 proteinopathies, how TDP-43 forms cytoplasmic aggregates remains unknown. In this study, we show that a deficiency in DCTN1, a subunit of the microtubule-associated motor protein complex dynactin, perturbs the dynamics of stress granules and drives the formation of TDP-43 cytoplasmic aggregation in cultured cells, leading to the exacerbation of TDP-43 pathology and neurodegeneration in vivo. We demonstrated using a Drosophila model of ALS/FTD that genetic knockdown of DCTN1 accelerates the formation of ubiquitin-positive cytoplasmic inclusions of TDP-43. Knockdown of components of other microtubule-associated motor protein complexes, including dynein and kinesin, also increased the formation of TDP-43 inclusions, indicating that intracellular transport along microtubules plays a key role in TDP-43 pathology. Notably, DCTN1 knockdown delayed the disassembly of stress granules in stressed cells, leading to an increase in the formation of pathological cytoplasmic inclusions of TDP-43. Our results indicate that a deficiency in DCTN1, as well as disruption of intracellular transport along microtubules, is a modifier that drives the formation of TDP-43 pathology through the dysregulation of stress granule dynamics.
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Affiliation(s)
- Tetsuhiro Ueda
- Department of Neurology, Faculty of Medicine, Kindai University, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
- Department of Neurology, Kyoto Prefectural University of Medicine, Kyoto, 602-0841, Japan
| | - Toshihide Takeuchi
- Life Science Research Institute, Kindai University, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan.
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan.
| | - Nobuhiro Fujikake
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Mari Suzuki
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Eiko N Minakawa
- Department of Neurophysiology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Morio Ueyama
- Department of Neurology, Faculty of Medicine, Kindai University, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Yuzo Fujino
- Department of Neurology, Faculty of Medicine, Kindai University, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
- Department of Neurology, Kyoto Prefectural University of Medicine, Kyoto, 602-0841, Japan
| | - Nobuyuki Kimura
- Department of Veterinary Associated Science, Faculty of Veterinary Medicine, Okayama University of Science, Ehime, 794-8555, Japan
| | - Seiichi Nagano
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Akio Yokoseki
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Osamu Onodera
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Toshiki Mizuno
- Department of Neurology, Kyoto Prefectural University of Medicine, Kyoto, 602-0841, Japan
| | - Keiji Wada
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Yoshitaka Nagai
- Department of Neurology, Faculty of Medicine, Kindai University, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan.
- Life Science Research Institute, Kindai University, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan.
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan.
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan.
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan.
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38
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D'Urso B, Weil R, Génin P. [Optineurin and mitochondrial dysfunction in neurodegeneration]. Med Sci (Paris) 2024; 40:167-175. [PMID: 38411425 DOI: 10.1051/medsci/2023220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
Optineurin (OPTN) is a multifunctional protein playing a crucial role as a receptor in selective autophagy. OPTN gene mutations are linked to diseases such as normal-tension glaucoma and amyotrophic lateral sclerosis. Recognized as a critical receptor for mitophagy, OPTN is pivotal in selectively degrading damaged mitochondria. This process is essential to prevent their accumulation, the generation of reactive oxygen species, and the release of pro-apoptotic factors. Mitophagy's quality control is governed by the PINK1 kinase and the cytosolic ubiquitin ligase Parkin, whose mutations are associated with Parkinson's disease. This review highlights recent insights emphasizing OPTN's role in mitophagy and its potential involvement in neurodegenerative diseases.
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Affiliation(s)
- Baptiste D'Urso
- CIMI-Paris, UPMC UMRS CR7 - Inserm U1135 - CNRS EMR8255, Faculté de médecine Sorbonne Université site Pitié-Salpêtrière, Paris, France - Sorbonne Université, Faculté des sciences et ingénierie, Paris, France
| | - Robert Weil
- CIMI-Paris, UPMC UMRS CR7 - Inserm U1135 - CNRS EMR8255, Faculté de médecine Sorbonne Université site Pitié-Salpêtrière, Paris, France
| | - Pierre Génin
- CIMI-Paris, UPMC UMRS CR7 - Inserm U1135 - CNRS EMR8255, Faculté de médecine Sorbonne Université site Pitié-Salpêtrière, Paris, France
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39
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Khalil B, Linsenmeier M, Smith CL, Shorter J, Rossoll W. Nuclear-import receptors as gatekeepers of pathological phase transitions in ALS/FTD. Mol Neurodegener 2024; 19:8. [PMID: 38254150 PMCID: PMC10804745 DOI: 10.1186/s13024-023-00698-1] [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: 06/05/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are fatal neurodegenerative disorders on a disease spectrum that are characterized by the cytoplasmic mislocalization and aberrant phase transitions of prion-like RNA-binding proteins (RBPs). The common accumulation of TAR DNA-binding protein-43 (TDP-43), fused in sarcoma (FUS), and other nuclear RBPs in detergent-insoluble aggregates in the cytoplasm of degenerating neurons in ALS/FTD is connected to nuclear pore dysfunction and other defects in the nucleocytoplasmic transport machinery. Recent advances suggest that beyond their canonical role in the nuclear import of protein cargoes, nuclear-import receptors (NIRs) can prevent and reverse aberrant phase transitions of TDP-43, FUS, and related prion-like RBPs and restore their nuclear localization and function. Here, we showcase the NIR family and how they recognize cargo, drive nuclear import, and chaperone prion-like RBPs linked to ALS/FTD. We also discuss the promise of enhancing NIR levels and developing potentiated NIR variants as therapeutic strategies for ALS/FTD and related neurodegenerative proteinopathies.
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Affiliation(s)
- Bilal Khalil
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
| | - Miriam Linsenmeier
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, U.S.A
| | - Courtney L Smith
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
- Mayo Clinic Graduate School of Biomedical Sciences, Neuroscience Track, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, U.S.A..
| | - Wilfried Rossoll
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A..
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40
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Rezvykh A, Shteinberg D, Bronovitsky E, Ustyugov A, Funikov S. Animal Models of FUS-Proteinopathy: A Systematic Review. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S34-S56. [PMID: 38621743 DOI: 10.1134/s0006297924140037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 04/17/2024]
Abstract
Mutations that disrupt the function of the DNA/RNA-binding protein FUS could cause amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases. One of the key features in ALS pathogenesis is the formation of insoluble protein aggregates containing aberrant isoforms of the FUS protein in the cytoplasm of upper and lower motor neurons. Reproduction of human pathology in animal models is the main tool for studying FUS-associated pathology and searching for potential therapeutic agents for ALS treatment. In this review, we provide a systematic analysis of the role of FUS protein in ALS pathogenesis and an overview of the results of modelling FUS-proteinopathy in animals.
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Affiliation(s)
- Alexander Rezvykh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Daniil Shteinberg
- Institute of Physiologically Active Compounds, Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, 142432, Russia
| | | | - Aleksey Ustyugov
- Institute of Physiologically Active Compounds, Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, 142432, Russia
| | - Sergei Funikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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41
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Shao Y, Shu X, Lu Y, Zhu W, Li R, Fu H, Li C, Sun W, Li Z, Zhang Y, Cao X, Ye X, Ajiboye E, Zhao B, Zhang L, Wu H, Feng XH, Yang B, Lu H. A chaperone-like function of FUS ensures TAZ condensate dynamics and transcriptional activation. Nat Cell Biol 2024; 26:86-99. [PMID: 38172614 DOI: 10.1038/s41556-023-01309-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024]
Abstract
The Hippo pathway has important roles in organ development, tissue homeostasis and tumour growth. Its downstream effector TAZ is a transcriptional coactivator that promotes target gene expression through the formation of biomolecular condensates. However, the mechanisms that regulate the biophysical properties of TAZ condensates to enable Hippo signalling are not well understood. Here using chemical crosslinking combined with an unbiased proteomics approach, we show that FUS associates with TAZ condensates and exerts a chaperone-like effect to maintain their proper liquidity and robust transcriptional activity. Mechanistically, the low complexity sequence domain of FUS targets the coiled-coil domain of TAZ in a phosphorylation-regulated manner, which ensures the liquidity and dynamicity of TAZ condensates. In cells lacking FUS, TAZ condensates transition into gel-like or solid-like assembles with immobilized TAZ, which leads to reduced expression of target genes and inhibition of pro-tumorigenic activity. Thus, our findings identify a chaperone-like function of FUS in Hippo regulation and demonstrate that appropriate biophysical properties of transcriptional condensates are essential for gene activation.
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Affiliation(s)
- Yangqing Shao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xin Shu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Yi Lu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wenxuan Zhu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Ran Li
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Huanyi Fu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Chengyu Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Wei Sun
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Zhuo Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yitong Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xiaolei Cao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xifu Ye
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Emmanuel Ajiboye
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, USA
| | - Bin Zhao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Long Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Haifan Wu
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, USA
| | - Xin-Hua Feng
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
| | - Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
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Mann N, Hill J, Wang K, Hughes RM. OptoProfilin: A Single Component Biosensor of Applied Cellular Stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.04.560945. [PMID: 37873064 PMCID: PMC10592976 DOI: 10.1101/2023.10.04.560945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The actin cytoskeleton is a biosensor of cellular stress and a potential prognosticator of human disease. In particular, aberrant cytoskeletal structures such as cofilin-actin rods and stress granules formed in response to energetic and oxidative stress are closely linked to neurodegenerative diseases such as Alzheimer's, Parkinson's, and ALS. Whether these cytoskeletal phenomena can be harnessed for the development of biosensors for cytoskeletal dysfunction and, by extension, neurodegenerative disease progression, remains an open question. In this work, we describe the design and development of an optogenetic iteration of profilin, an actin monomer binding protein with critical functions in cytoskeletal dynamics. We demonstrate that this optically activated profilin ('OptoProfilin') can act as an optically triggered biosensor of applied cellular stress in select immortalized cell lines. Notably, OptoProfilin is a single component biosensor, likely increasing its utility for experimentalists. While a large body of preexisting work closely links profilin activity with cellular stress and neurodegenerative disease, this, to our knowledge, is the first example of profilin as an optogenetic biosensor of stress-induced changes in the cytoskeleton.
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Affiliation(s)
- Noah Mann
- Department of Chemistry, East Carolina University, Greenville, North Carolina, United States
| | - Jahiem Hill
- Department of Chemistry, East Carolina University, Greenville, North Carolina, United States
| | - Kenneth Wang
- Department of Chemistry, Davidson College, Davidson, North Carolina, United States
| | - Robert M. Hughes
- Department of Chemistry, East Carolina University, Greenville, North Carolina, United States
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43
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Dhakal S, Mondal M, Mirzazadeh A, Banerjee S, Ghosh A, Rangachari V. α-Synuclein emulsifies TDP-43 prion-like domain-RNA liquid droplets to promote heterotypic amyloid fibrils. Commun Biol 2023; 6:1227. [PMID: 38052886 PMCID: PMC10697960 DOI: 10.1038/s42003-023-05608-1] [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: 09/06/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
Many neurodegenerative diseases including frontotemporal lobar degeneration (FTLD), Lewy body disease (LBD), multiple system atrophy (MSA), etc., show colocalized deposits of TDP-43 and α-synuclein (αS) aggregates. To understand whether these colocalizations are driven by specific molecular interactions between the two proteins, we previously showed that the prion-like C-terminal domain of TDP-43 (TDP-43PrLD) and αS synergistically interact to form neurotoxic heterotypic amyloids in homogeneous buffer conditions. However, it remains unclear if αS can modulate TDP-43 present within liquid droplets and biomolecular condensates called stress granules (SGs). Here, using cell culture and in vitro TDP-43PrLD - RNA liquid droplets as models along with microscopy, nanoscale AFM-IR spectroscopy, and biophysical analyses, we uncover the interactions of αS with phase-separated droplets. We learn that αS acts as a Pickering agent by forming clusters on the surface of TDP-43PrLD - RNA droplets. The aggregates of αS on these clusters emulsify the droplets by nucleating the formation of heterotypic TDP-43PrLD amyloid fibrils, structures of which are distinct from those derived from homogenous solutions. Together, these results reveal an intriguing property of αS to act as a Pickering agent while interacting with SGs and unmask the hitherto unknown role of αS in modulating TDP-43 proteinopathies.
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Affiliation(s)
- Shailendra Dhakal
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Malay Mondal
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Azin Mirzazadeh
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Siddhartha Banerjee
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL, 35401, USA
| | - Ayanjeet Ghosh
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL, 35401, USA
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS, 39406, USA.
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS, 39406, USA.
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44
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Redding A, Grabocka E. Stress granules and hormetic adaptation of cancer. Trends Cancer 2023; 9:995-1005. [PMID: 37704502 PMCID: PMC10843007 DOI: 10.1016/j.trecan.2023.08.005] [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: 04/04/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
Cell stress is inherent to cancer and a key driver of tumorigenesis. Recent studies have proposed that cell stress promotes tumorigenesis through non-membranous organelles known as stress granules (SGs). While the biology of SGs is an emerging field, all studies to date point to the enhanced ability of cancer cells to form SGs compared with normal cells, a heightened dependence on SGs for survival under adverse conditions and for chemotherapy resistance, and the dependence of tumors on SGs for growth. Why cancer cells become dependent on SGs and how SGs promote tumorigenesis remain to be elucidated. Here, we attempt to provide a framework for answering these questions by framing SGs as a hormetic response to tumor-associated stress stimuli.
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Affiliation(s)
- Alexandra Redding
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Elda Grabocka
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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45
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Babazadeh A, Rayner SL, Lee A, Chung RS. TDP-43 as a therapeutic target in neurodegenerative diseases: Focusing on motor neuron disease and frontotemporal dementia. Ageing Res Rev 2023; 92:102085. [PMID: 37813308 DOI: 10.1016/j.arr.2023.102085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023]
Abstract
A common feature of adult-onset neurodegenerative diseases is the presence of characteristic pathological accumulations of specific proteins. These pathological protein depositions can vary in their protein composition, cell-type distribution, and intracellular (or extracellular) location. For example, abnormal cytoplasmic protein deposits which consist of the TDP-43 protein are found within motor neurons in patients with amyotrophic lateral sclerosis (ALS, a common form of motor neuron disease) and frontotemporal dementia (FTD). The presence of these insoluble intracellular TDP-43 inclusions suggests that restoring TDP-43 homeostasis represents a potential therapeutical strategy, which has been demonstrated in alleviating neurodegenerative symptoms in cell and animal models of ALS/FTD. We have reviewed the mechanisms that lead to disrupted TDP-43 homeostasis and discussed how small molecule-based therapies could be applied in modulating these mechanisms. This review covers recent advancements and challenges in small molecule-based therapies that could be used to clear pathological forms of TDP-43 through various protein homeostasis mechanisms and advance the way towards finding effective therapeutical drug discoveries for neurodegenerative diseases characterized by TDP-43 proteinopathies, especially ALS and FTD. We also consider the wider insight of these therapeutic strategies for other neurodegenerative diseases.
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Affiliation(s)
- Afshin Babazadeh
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Stephanie L Rayner
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Albert Lee
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Roger S Chung
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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46
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Elmansy MF, Reidl CT, Rahaman M, Özdinler PH, Silverman RB. Small molecules targeting different cellular pathologies for the treatment of amyotrophic lateral sclerosis. Med Res Rev 2023; 43:2260-2302. [PMID: 37243319 PMCID: PMC10592673 DOI: 10.1002/med.21974] [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: 04/28/2022] [Revised: 02/28/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease in which the motor neuron circuitry displays progressive degeneration, affecting mostly the motor neurons in the brain and in the spinal cord. There are no effective cures, albeit three drugs, riluzole, edaravone, and AMX0035 (a combination of sodium phenylbutyrate and taurursodiol), have been approved by the Food and Drug Administration, with limited improvement in patients. There is an urgent need to build better and more effective treatment strategies for ALS. Since the disease is very heterogenous, numerous approaches have been explored, such as targeting genetic mutations, decreasing oxidative stress and excitotoxicity, enhancing mitochondrial function and protein degradation mechanisms, and inhibiting neuroinflammation. In addition, various chemical libraries or previously identified drugs have been screened for potential repurposing in the treatment of ALS. Here, we review previous drug discovery efforts targeting a variety of cellular pathologies that occur from genetic mutations that cause ALS, such as mutations in SOD1, C9orf72, FUS, and TARDP-43 genes. These mutations result in protein aggregation, which causes neuronal degeneration. Compounds used to target cellular pathologies that stem from these mutations are discussed and comparisons among different preclinical models are presented. Because the drug discovery landscape for ALS and other motor neuron diseases is changing rapidly, we also offer recommendations for a novel, more effective, direction in ALS drug discovery that could accelerate translation of effective compounds from animals to patients.
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Affiliation(s)
- Mohamed F. Elmansy
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois, USA
- Department of Organometallic and Organometalloid Chemistry, National Research Centre, Cairo, Egypt
| | - Cory T. Reidl
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois, USA
| | - Mizzanoor Rahaman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois, USA
| | - P. Hande Özdinler
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Richard B. Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois, USA
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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47
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Hu ML, Pan YR, Yong YY, Liu Y, Yu L, Qin DL, Qiao G, Law BYK, Wu JM, Zhou XG, Wu AG. Poly (ADP-ribose) polymerase 1 and neurodegenerative diseases: Past, present, and future. Ageing Res Rev 2023; 91:102078. [PMID: 37758006 DOI: 10.1016/j.arr.2023.102078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 08/30/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) is a first responder that recognizes DNA damage and facilitates its repair. Neurodegenerative diseases, characterized by progressive neuron loss driven by various risk factors, including DNA damage, have increasingly shed light on the pivotal involvement of PARP1. During the early phases of neurodegenerative diseases, PARP1 experiences controlled activation to swiftly address mild DNA damage, thereby contributing to maintain brain homeostasis. However, in late stages, exacerbated PARP1 activation precipitated by severe DNA damage exacerbates the disease condition. Consequently, inhibition of PARP1 overactivation emerges as a promising therapeutic approach for neurodegenerative diseases. In this review, we comprehensively synthesize and explore the multifaceted role of PARP1 in neurodegenerative diseases, with a particular emphasis on its over-activation in the aggregation of misfolded proteins, dysfunction of the autophagy-lysosome pathway, mitochondrial dysfunction, neuroinflammation, and blood-brain barrier (BBB) injury. Additionally, we encapsulate the therapeutic applications and limitations intrinsic of PARP1 inhibitors, mainly including limited specificity, intricate pathway dynamics, constrained clinical translation, and the heterogeneity of patient cohorts. We also explore and discuss the potential synergistic implementation of these inhibitors alongside other agents targeting DNA damage cascades within neurodegenerative diseases. Simultaneously, we propose several recommendations for the utilization of PARP1 inhibitors within the realm of neurodegenerative disorders, encompassing factors like the disease-specific roles of PARP1, combinatorial therapeutic strategies, and personalized medical interventions. Lastly, the encompassing review presents a forward-looking perspective along with strategic recommendations that could guide future research endeavors in this field.
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Affiliation(s)
- Meng-Ling Hu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Yi-Ru Pan
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Yuan-Yuan Yong
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Yi Liu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Lu Yu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Da-Lian Qin
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Gan Qiao
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Betty Yuen-Kwan Law
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Jian-Ming Wu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China.
| | - Xiao-Gang Zhou
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China.
| | - An-Guo Wu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China.
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48
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Jiang N, Li W, Jiang S, Xie M, Liu R. Acetylation in pathogenesis: Revealing emerging mechanisms and therapeutic prospects. Biomed Pharmacother 2023; 167:115519. [PMID: 37729729 DOI: 10.1016/j.biopha.2023.115519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 09/22/2023] Open
Abstract
Protein acetylation modifications play a central and pivotal role in a myriad of biological processes, spanning cellular metabolism, proliferation, differentiation, apoptosis, and beyond, by effectively reshaping protein structure and function. The metabolic state of cells is intricately connected to epigenetic modifications, which in turn influence chromatin status and gene expression patterns. Notably, pathological alterations in protein acetylation modifications are frequently observed in diseases such as metabolic syndrome, cardiovascular disorders, and cancer. Such abnormalities can result in altered protein properties and loss of function, which are closely associated with developing and progressing related diseases. In recent years, the advancement of precision medicine has highlighted the potential value of protein acetylation in disease diagnosis, treatment, and prevention. This review includes provocative and thought-provoking papers outlining recent breakthroughs in acetylation modifications as they relate to cardiovascular disease, mitochondrial metabolic regulation, liver health, neurological health, obesity, diabetes, and cancer. Additionally, it covers the molecular mechanisms and research challenges in understanding the role of acetylation in disease regulation. By summarizing novel targets and prognostic markers for the treatment of related diseases, we aim to contribute to the field. Furthermore, we discuss current hot topics in acetylation research related to health regulation, including N4-acetylcytidine and liquid-liquid phase separation. The primary objective of this review is to provide insights into the functional diversity and underlying mechanisms by which acetylation regulates proteins in disease contexts.
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Affiliation(s)
- Nan Jiang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Wenyong Li
- School of Biology and Food Engineering, Fuyang Normal University, Fuyang, Anhui 236037, China
| | - Shuanglin Jiang
- School of Biology and Food Engineering, Fuyang Normal University, Fuyang, Anhui 236037, China
| | - Ming Xie
- North China Petroleum Bureau General Hospital, Renqiu 062550, China.
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
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49
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Webber CJ, Murphy CN, Rondón-Ortiz AN, van der Spek SJF, Kelly EX, Lampl NM, Chiesa G, Khalil AS, Emili A, Wolozin B. Human herpesvirus 8 ORF57 protein is able to reduce TDP-43 pathology: network analysis identifies interacting pathways. Hum Mol Genet 2023; 32:2966-2980. [PMID: 37522762 PMCID: PMC10549787 DOI: 10.1093/hmg/ddad122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023] Open
Abstract
Aggregation of TAR DNA-binding protein 43 kDa (TDP-43) is thought to drive the pathophysiology of amyotrophic lateral sclerosis and some frontotemporal dementias. TDP-43 is normally a nuclear protein that in neurons translocates to the cytoplasm and can form insoluble aggregates upon activation of the integrated stress response (ISR). Viruses evolved to control the ISR. In the case of Herpesvirus 8, the protein ORF57 acts to bind protein kinase R, inhibit phosphorylation of eIF2α and reduce activation of the ISR. We hypothesized that ORF57 might also possess the ability to inhibit aggregation of TDP-43. ORF57 was expressed in the neuronal SH-SY5Y line and its effects on TDP-43 aggregation characterized. We report that ORF57 inhibits TDP-43 aggregation by 55% and elicits a 2.45-fold increase in the rate of dispersion of existing TDP-43 granules. These changes were associated with a 50% decrease in cell death. Proteomic studies were carried out to identify the protein interaction network of ORF57. We observed that ORF57 directly binds to TDP-43 as well as interacts with many components of the ISR, including elements of the proteostasis machinery known to reduce TDP-43 aggregation. We propose that viral proteins designed to inhibit a chronic ISR can be engineered to remove aggregated proteins and dampen a chronic ISR.
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Affiliation(s)
- Chelsea J Webber
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
| | - Caroline N Murphy
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
| | - Alejandro N Rondón-Ortiz
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Sophie J F van der Spek
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
| | - Elena X Kelly
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
| | - Noah M Lampl
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
| | - Giulio Chiesa
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biochemistry, Boston University, Boston, MA 02115, USA
- Department of Biochemistry, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Benjamin Wolozin
- Departments of Pharmacology, Physiology and Biophysics, Boston University, Boston, MA 02215, USA
- Center for Systems Neuroscience, Boston University, Boston, MA 02115, USA
- Center for Neurophotonics, Boston University, Boston, MA 02115, USA
- Department of Neurology, Boston University, Boston, MA 02115, USA
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50
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Mukhopadhyay C, Zhou P. Role(s) of G3BPs in Human Pathogenesis. J Pharmacol Exp Ther 2023; 387:100-110. [PMID: 37468286 PMCID: PMC10519580 DOI: 10.1124/jpet.122.001538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 06/28/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023] Open
Abstract
Ras-GTPase-activating protein (SH3 domain)-binding proteins (G3BP) are RNA binding proteins that play a critical role in stress granule (SG) formation. SGs protect critical mRNAs from various environmental stress conditions by regulating mRNA stability and translation to maintain regulated gene expression. Recent evidence suggests that G3BPs can also regulate mRNA expression through interactions with RNA outside of SGs. G3BPs have been associated with a number of disease states, including cancer progression, invasion, metastasis, and viral infections, and may be useful as a cancer therapeutic target. This review summarizes the biology of G3BP including their structure, function, localization, role in cancer progression, virus replication, mRNA stability, and SG formation. We will also discuss the potential of G3BPs as a therapeutic target. SIGNIFICANCE STATEMENT: This review will discuss the molecular mechanism(s) and functional role(s) of Ras-GTPase-activating protein (SH3 domain)-binding proteins in the context of stress granule formation, interaction with viruses, stability of RNA, and tumorigenesis.
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Affiliation(s)
- Chandrani Mukhopadhyay
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York
| | - Pengbo Zhou
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York
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