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Eibauer M, Weber MS, Kronenberg-Tenga R, Beales CT, Boujemaa-Paterski R, Turgay Y, Sivagurunathan S, Kraxner J, Köster S, Goldman RD, Medalia O. Vimentin filaments integrate low-complexity domains in a complex helical structure. Nat Struct Mol Biol 2024:10.1038/s41594-024-01261-2. [PMID: 38632361 DOI: 10.1038/s41594-024-01261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Intermediate filaments (IFs) are integral components of the cytoskeleton. They provide cells with tissue-specific mechanical properties and are involved in numerous cellular processes. Due to their intricate architecture, a 3D structure of IFs has remained elusive. Here we use cryo-focused ion-beam milling, cryo-electron microscopy and tomography to obtain a 3D structure of vimentin IFs (VIFs). VIFs assemble into a modular, intertwined and flexible helical structure of 40 α-helices in cross-section, organized into five protofibrils. Surprisingly, the intrinsically disordered head domains form a fiber in the lumen of VIFs, while the intrinsically disordered tails form lateral connections between the protofibrils. Our findings demonstrate how protein domains of low sequence complexity can complement well-folded protein domains to construct a biopolymer with striking mechanical strength and stretchability.
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Affiliation(s)
- Matthias Eibauer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Miriam S Weber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Charlie T Beales
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Yagmur Turgay
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Suganya Sivagurunathan
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Julia Kraxner
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
- MDC Berlin-Buch, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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2
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Goldman RD, Hart RJ, Bone JN, Seiler M, Olson PG, Keitel K, Manzano S, Gualco G, Krupik D, Schroter S, Weigert RM, Chung S, Thompson GC, Muhammad N, Shah P, Gaucher NO, Hou M, Griffiths J, Lunoe MM, Evers M, Pharisa Rochat C, Nelson CE, Gal M, Baumer-Mouradian SH. Willingness to vaccinate children against COVID-19 declined during the pandemic. Vaccine 2023; 41:2495-2502. [PMID: 36889992 PMCID: PMC9977620 DOI: 10.1016/j.vaccine.2023.02.069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 02/08/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023]
Abstract
OBJECTIVES To document the level of vaccine hesitancy in caregivers' of children younger than 12 years of age over the course of the pandemic in Pediatric Emergency Departments (ED). Study design Ongoing multicenter, cross-sectional survey of caregivers presenting to 19 pediatric EDs in the USA, Canada, Israel, and Switzerland during first months of the pandemic (phase1), when vaccines were approved for adults (phase2) and most recently when vaccines were approved for children (phase3). RESULTS Willingness to vaccinate rate declined over the study period (59.7%, 56.1% and 52.1% in the three phases). Caregivers who are fully vaccinated, who have higher education, and those worried their child had COVID-19 upon arrival to the ED, were more likely to plan to vaccinate in all three phases. Mothers were less likely to vaccinate early in the pandemic, but this hesitancy attenuated in later phases. Older caregivers were more willing to vaccinate, and caregivers of older children were less likely to vaccinate their children in phase 3. During the last phase, willingness to vaccinate was lowest in those who had a primary care provider but did not rely on their advice for medical decisions (34%). Those with no primary care provider and those who do and rely on their medical advice, had similar rates of willingness to vaccinate (55.1% and 52.1%, respectively). CONCLUSIONS COVID-19 vaccine hesitancy is widespread and growing over time, and public health measures should further try to leverage identified factors associated with hesitancy in order to enhance vaccination rates among children.
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Affiliation(s)
- R D Goldman
- The Pediatric Research in Emergency Therapeutics (PRETx) Program, Division of Emergency Medicine, Department of Pediatrics, University of British Columbia, and BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.
| | - R J Hart
- Division of Pediatric Emergency Medicine, Department of Pediatrics, University of Louisville, Louisville, KY, USA
| | - J N Bone
- Research Informatics, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - M Seiler
- Emergency Department, University Children's Hospital Zurich, Zurich, Switzerland
| | - P G Olson
- Department of Pediatrics, Division of Emergency and Transport Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - K Keitel
- Pediatric Emergency Medicine, Inselspital University Hospital of Bern, Bern, Switzerland
| | - S Manzano
- Department of Pediatric Emergency Medicine, Geneva Children's Hospital, Geneva University Hospitals, and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - G Gualco
- Pediatric Emergency Department, Pediatric Institute of Italian part of Switzerland, Ticino, Switzerland
| | - D Krupik
- Pediatric Emergency Unit, Ziv Medical Center, and Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - S Schroter
- Division of Pediatric Emergency Medicine, Department of Pediatrics, University of California, San Diego, La Jolla, California and Rady Children's Hospital San Diego, San Diego, CA, USA
| | - R M Weigert
- Department of Pediatric Emergency Medicine, Children's Minnesota, Minneapolis, MN, USA
| | - S Chung
- Pediatric Emergency Medicine, Oregon Health & Science University, Portland, OR, USA
| | - G C Thompson
- Pediatrics and Emergency Medicine, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - N Muhammad
- Division of Pediatric Emergency Medicine, Advocate Children's Hospital, Oak Lawn, IL, USA
| | - P Shah
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA
| | - N O Gaucher
- Department of Pediatric Emergency Medicine and Research Center, Department of Pediatrics, CHU Sainte-Justine, 3175 Ch Cote Sainte-Catherine, Montreal, Canada
| | - M Hou
- The Pediatric Research in Emergency Therapeutics (PRETx) Program, Division of Emergency Medicine, Department of Pediatrics, University of British Columbia, and BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - J Griffiths
- The Pediatric Research in Emergency Therapeutics (PRETx) Program, Division of Emergency Medicine, Department of Pediatrics, University of British Columbia, and BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - M M Lunoe
- Division of Pediatric Emergency Medicine, UPMC Children's Hospital of Pittsburgh, PA, USA
| | - M Evers
- Division of Pediatric Pediatric Emergency Medicine, UH Rainbow Babies and Children's Hospital, 11100 Euclid Ave, Cleveland, OH, USA
| | - C Pharisa Rochat
- Division of Pediatric Emergency Medicine, Department of Pediatrics, Fribourg Hospital HFR, Fribourg, Switzerland
| | - C E Nelson
- Division of Emergency Medicine, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Wilmington, DE, USA
| | - M Gal
- Pediatric Emergency Department, Kaplan Medical Centre, Rehovot, Israel
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Kono Y, Adam SA, Sato Y, Reddy KL, Zheng Y, Medalia O, Goldman RD, Kimura H, Shimi T. Nucleoplasmic lamin C rapidly accumulates at sites of nuclear envelope rupture with BAF and cGAS. J Cell Biol 2022; 221:213616. [PMID: 36301259 PMCID: PMC9617480 DOI: 10.1083/jcb.202201024] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 07/14/2022] [Accepted: 09/06/2022] [Indexed: 12/13/2022] Open
Abstract
In mammalian cell nuclei, the nuclear lamina (NL) underlies the nuclear envelope (NE) to maintain nuclear structure. The nuclear lamins, the major structural components of the NL, are involved in the protection against NE rupture induced by mechanical stress. However, the specific role of the lamins in repair of NE ruptures has not been fully determined. Our analyses using immunofluorescence and live-cell imaging revealed that the nucleoplasmic pool of lamin C rapidly accumulated at sites of NE rupture induced by laser microirradiation in mouse embryonic fibroblasts. The accumulation of lamin C at the rupture sites required both the immunoglobulin-like fold domain that binds to barrier-to-autointegration factor (BAF) and a nuclear localization signal. The accumulation of nuclear BAF and cytoplasmic cyclic GMP-AMP synthase (cGAS) at the rupture sites was in part dependent on lamin A/C. These results suggest that nucleoplasmic lamin C, BAF, and cGAS concertedly accumulate at sites of NE rupture for rapid repair.
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Affiliation(s)
- Yohei Kono
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Stephen A Adam
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Yuko Sato
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Karen L Reddy
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD
| | - Yixian Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Takeshi Shimi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.,World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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Stenvall CGA, Nyström JH, Butler-Hallissey C, Jansson T, Heikkilä TRH, Adam SA, Foisner R, Goldman RD, Ridge KM, Toivola DM. Cytoplasmic keratins couple with and maintain nuclear envelope integrity in colonic epithelial cells. Mol Biol Cell 2022; 33:ar121. [PMID: 36001365 PMCID: PMC9634972 DOI: 10.1091/mbc.e20-06-0387] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Keratin intermediate filaments convey mechanical stability and protection against stress to epithelial cells. Keratins are essential for colon health, as seen in keratin 8 knockout (K8-/-) mice exhibiting a colitis phenotype. We hypothesized that keratins support the nuclear envelope and lamina in colonocytes. K8-/- colonocytes in vivo exhibit significantly decreased levels of lamins A/C, B1, and B2 in a colon-specific and cell-intrinsic manner. CRISPR/Cas9- or siRNA-mediated K8 knockdown in Caco-2 cells similarly decreased lamin levels, which recovered after reexpression of K8 following siRNA treatment. Nuclear area was not decreased, and roundness was only marginally increased in cells without K8. Down-regulation of K8 in adult K8flox/flox;Villin-CreERt2 mice following tamoxifen administration significantly decreased lamin levels at day 4 when K8 levels had reduced to 40%. K8 loss also led to reduced levels of plectin, LINC complex, and lamin-associated proteins. While keratins were not seen in the nucleoplasm without or with leptomycin B treatment, keratins were found intimately located at the nuclear envelope and complexed with SUN2 and lamin A. Furthermore, K8 loss in Caco-2 cells compromised nuclear membrane integrity basally and after shear stress. In conclusion, colonocyte K8 helps maintain nuclear envelope and lamina composition and contributes to nuclear integrity.
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Affiliation(s)
| | - Joel H. Nyström
- Cell Biology, Biosciences, Faculty of Science and Engineering, Åbo Akademi University
| | - Ciarán Butler-Hallissey
- Cell Biology, Biosciences, Faculty of Science and Engineering, Åbo Akademi University,Turku Bioscience Centre, University of Turku, and Åbo Akademi University, and,Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, 13005 Marseille, France
| | - Theresia Jansson
- Cell Biology, Biosciences, Faculty of Science and Engineering, Åbo Akademi University
| | - Taina R. H. Heikkilä
- Cell Biology, Biosciences, Faculty of Science and Engineering, Åbo Akademi University
| | | | - Roland Foisner
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter Campus, 1030 Vienna, Austria
| | | | - Karen M. Ridge
- Department of Cell and Developmental Biology and,Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Diana M. Toivola
- Cell Biology, Biosciences, Faculty of Science and Engineering, Åbo Akademi University,InFLAMES Research Flagship Center, Åbo Akademi University, 20500 Turku, Finland,Turku Center for Disease Modeling, University of Turku, 20520 Turku, Finland,*Address correspondence to: Diana M. Toivola ()
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5
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Tran JR, Zheng X, Adam SA, Goldman RD, Zheng Y. High quality mapping of chromatin at or near the nuclear lamina from small numbers of cells reveals cell cycle and developmental changes of chromatin at the nuclear periphery. Nucleic Acids Res 2022; 50:e117. [PMID: 36130229 PMCID: PMC9723609 DOI: 10.1093/nar/gkac762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 07/28/2022] [Accepted: 09/16/2022] [Indexed: 12/24/2022] Open
Abstract
The chromatin associated with the nuclear lamina (NL) is referred to as lamina-associated domains (LADs). Here, we present an adaptation of the tyramide-signal amplification sequencing (TSA-seq) protocol, which we call chromatin pull down-based TSA-seq (cTSA-seq), that can be used to map chromatin regions at or near the NL from as little as 50 000 cells. The cTSA-seq mapped regions are composed of previously defined LADs and smaller chromatin regions that fall within the Hi-C defined B-compartment containing nuclear peripheral heterochromatin. We used cTSA-seq to map chromatin at or near the assembling NL in cultured cells progressing through early G1. cTSA-seq revealed that the distal ends of chromosomes are near or at the reassembling NL during early G1, a feature similar to those found in senescent cells. We expand the use of cTSA-seq to the mapping of chromatin at or near the NL from fixed-frozen mouse cerebellar tissue sections. This mapping reveals a general conservation of NL-associated chromatin and identifies global and local changes during cerebellar development. The cTSA-seq method reported here is useful for analyzing chromatin at or near the NL from small numbers of cells derived from both in vitro and in vivo sources.
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Affiliation(s)
- Joseph R Tran
- Correspondence may also be addressed to Joseph R. Tran. Tel: +1 410 246 3032; Fax: +1 410 243 6311;
| | - Xiaobin Zheng
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA
| | - Stephen A Adam
- Department of Cell and Developmental Biology, Northwestern University, Feinberg School of Medicine, Ward Building 11-145, 303 E. Chicago Ave. Chicago, IL 60611, USA
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Northwestern University, Feinberg School of Medicine, Ward Building 11-145, 303 E. Chicago Ave. Chicago, IL 60611, USA
| | - Yixian Zheng
- To whom correspondence should be addressed. Tel: +1 410 246 3032; Fax: +1 410 243 6311;
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6
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Sivagurunathan S, Vahabikashi A, Yang H, Zhang J, Vazquez K, Rajasundaram D, Politanska Y, Abdala-Valencia H, Notbohm J, Guo M, Adam SA, Goldman RD. Expression of vimentin alters cell mechanics, cell-cell adhesion, and gene expression profiles suggesting the induction of a hybrid EMT in human mammary epithelial cells. Front Cell Dev Biol 2022; 10:929495. [PMID: 36200046 PMCID: PMC9527304 DOI: 10.3389/fcell.2022.929495] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Vimentin is a Type III intermediate filament (VIF) cytoskeletal protein that regulates the mechanical and migratory behavior of cells. Its expression is considered to be a marker for the epithelial to mesenchymal transition (EMT) that takes place in tumor metastasis. However, the molecular mechanisms regulated by the expression of vimentin in the EMT remain largely unexplored. We created MCF7 epithelial cell lines expressing vimentin from a cumate-inducible promoter to address this question. When vimentin expression was induced in these cells, extensive cytoplasmic VIF networks were assembled accompanied by changes in the organization of the endogenous keratin intermediate filament networks and disruption of desmosomes. Significant reductions in intercellular forces by the cells expressing VIFs were measured by quantitative monolayer traction force and stress microscopy. In contrast, laser trapping micro-rheology revealed that the cytoplasm of MCF7 cells expressing VIFs was stiffer than the uninduced cells. Vimentin expression activated transcription of genes involved in pathways responsible for cell migration and locomotion. Importantly, the EMT related transcription factor TWIST1 was upregulated only in wild type vimentin expressing cells and not in cells expressing a mutant non-polymerized form of vimentin, which only formed unit length filaments (ULF). Taken together, our results suggest that vimentin expression induces a hybrid EMT correlated with the upregulation of genes involved in cell migration.
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Affiliation(s)
- Suganya Sivagurunathan
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Amir Vahabikashi
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Haiqian Yang
- Department of Mechanical Engineering , Massachusetts Institute of Technology , Cambridge , MA, United States
| | - Jun Zhang
- Biophysics Program, University of Wisconsin-Madison, Madison, WI, United States
- Department of Engineering Physics, University of Wisconsin-Madison, Madison, WI, United States
| | - Kelly Vazquez
- Department of Engineering Physics, University of Wisconsin-Madison, Madison, WI, United States
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Yuliya Politanska
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Hiam Abdala-Valencia
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Jacob Notbohm
- Biophysics Program, University of Wisconsin-Madison, Madison, WI, United States
- Department of Engineering Physics, University of Wisconsin-Madison, Madison, WI, United States
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Ming Guo
- Department of Mechanical Engineering , Massachusetts Institute of Technology , Cambridge , MA, United States
| | - Stephen A Adam
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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7
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Goldman RD, Seiler M, Olson PG, Hart RJ, Bone JN, Baumer-Mouradian SH. Factors associated with unvaccinated caregivers who plan to vaccinate their children. Prev Med 2022; 162:107121. [PMID: 35863584 PMCID: PMC9290374 DOI: 10.1016/j.ypmed.2022.107121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/24/2022] [Accepted: 06/15/2022] [Indexed: 12/02/2022]
Abstract
Vaccine hesitancy is complex and a threat to global public health during the ongoing COVID-19 pandemic. Our objective was to determine factors associated with caregivers' willingness to vaccinate children despite not being immunized themselves against COVID-19. The International COVID-19 Parental Attitude Study (COVIPAS), a multinational cohort study, recruited caregivers of children 0-18 years old in 21 Emergency Departments (EDs) in USA, Canada, Israel, and Switzerland during November-December 2021. Of a total of 4536 caregivers who completed the survey, 882 (19.4%) were unvaccinated, and 62 (7.0%) of the unvaccinated planned to vaccinate their children. Unvaccinated caregivers with children that had their childhood vaccines up-to-date (OR 3.03 (1.36, 8.09), p = 0.01), and those very worried their child has COVID-19 in the ED (OR 3.11 (1.44, 6.34), p < 0.01) were much more likely to plan to immunize their children. Primary care providers and public health agencies should not assume that unvaccinated parents will not vaccinate their children. Determining child's vaccination status and parental level of concern about COVID-19 may help identify caregivers who are open to give their children the vaccine.
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Affiliation(s)
- R D Goldman
- The Pediatric Research in Emergency Therapeutics (PRETx) Program, Division of Emergency Medicine, Department of Pediatrics, University of British Columbia, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.
| | - M Seiler
- Emergency Department, University Children's Hospital Zurich, Zurich, Switzerland.
| | - P G Olson
- Department of Pediatrics, Division of Emergency and Transport Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States.
| | - R J Hart
- Division of Pediatric Emergency Medicine, Department of Pediatrics, University of Louisville, Louisville, KY, United States.
| | - J N Bone
- Research Informatics, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.
| | - S H Baumer-Mouradian
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States.
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Abstract
More than 27 yr ago, the vimentin knockout (Vim-/- ) mouse was reported to develop and reproduce without an obvious phenotype, implying that this major cytoskeletal protein was nonessential. Subsequently, comprehensive and careful analyses have revealed numerous phenotypes in Vim-/- mice and their organs, tissues, and cells, frequently reflecting altered responses in the recovery of tissues following various insults or injuries. These findings have been supported by cell-based experiments demonstrating that vimentin intermediate filaments (IFs) play a critical role in regulating cell mechanics and are required to coordinate mechanosensing, transduction, signaling pathways, motility, and inflammatory responses. This review highlights the essential functions of vimentin IFs revealed from studies of Vim-/- mice and cells derived from them.
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Affiliation(s)
- Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois 60611, USA
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois 60611, USA
| | - John E Eriksson
- Cell Biology, Faculty of Science and Technology, Åbo Akademi University, FIN-20521 Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20521 Turku, Finland
- Euro-Bioimaging European Research Infrastructure Consortium (ERIC), FIN-20521 Turku, Finland
| | - Milos Pekny
- Laboratory of Astrocyte Biology and CNS Regeneration, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, 413 90 Gothenburg, Sweden
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria 3052, Australia
- University of Newcastle, Newcastle, New South Wales 2300, Australia
| | - Robert D Goldman
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois 60611, USA
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois 60611, USA
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9
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Vahabikashi A, Adam SA, Medalia O, Goldman RD. Nuclear lamins: Structure and function in mechanobiology. APL Bioeng 2022; 6:011503. [PMID: 35146235 PMCID: PMC8810204 DOI: 10.1063/5.0082656] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/11/2022] [Indexed: 12/11/2022] Open
Abstract
Nuclear lamins are type V intermediate filament proteins that polymerize into complex filamentous meshworks at the nuclear periphery and in less structured forms throughout the nucleoplasm. Lamins interact with a wide range of nuclear proteins and are involved in numerous nuclear and cellular functions. Within the nucleus, they play roles in chromatin organization and gene regulation, nuclear shape, size, and mechanics, and the organization and anchorage of nuclear pore complexes. At the whole cell level, they are involved in the organization of the cytoskeleton, cell motility, and mechanotransduction. The expression of different lamin isoforms has been associated with developmental progression, differentiation, and tissue-specific functions. Mutations in lamins and their binding proteins result in over 15 distinct human diseases, referred to as laminopathies. The laminopathies include muscular (e.g., Emery-Dreifuss muscular dystrophy and dilated cardiomyopathy), neurological (e.g., microcephaly), and metabolic (e.g., familial partial lipodystrophy) disorders as well as premature aging diseases (e.g., Hutchinson-Gilford Progeria and Werner syndromes). How lamins contribute to the etiology of laminopathies is still unknown. In this review article, we summarize major recent findings on the structure, organization, and multiple functions of lamins in nuclear and more global cellular processes.
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Affiliation(s)
- Amir Vahabikashi
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Stephen A. Adam
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Robert D. Goldman
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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10
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Weber MS, Eibauer M, Sivagurunathan S, Magin TM, Goldman RD, Medalia O. Structural heterogeneity of cellular K5/K14 filaments as revealed by cryo-electron microscopy. eLife 2021; 10:70307. [PMID: 34323216 PMCID: PMC8360650 DOI: 10.7554/elife.70307] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/23/2021] [Indexed: 12/11/2022] Open
Abstract
Keratin intermediate filaments are an essential and major component of the cytoskeleton in epithelial cells. They form a stable yet dynamic filamentous network extending from the nucleus to the cell periphery, which provides resistance to mechanical stresses. Mutations in keratin genes are related to a variety of epithelial tissue diseases. Despite their importance, the molecular structure of keratin filaments remains largely unknown. In this study, we analyzed the structure of keratin 5/keratin 14 filaments within ghost mouse keratinocytes by cryo-electron microscopy and cryo-electron tomography. By averaging a large number of keratin segments, we have gained insights into the helical architecture of the filaments. Two-dimensional classification revealed profound variations in the diameter of keratin filaments and their subunit organization. Computational reconstitution of filaments of substantial length uncovered a high degree of internal heterogeneity along single filaments, which can contain regions of helical symmetry, regions with less symmetry and regions with significant diameter fluctuations. Cross-section views of filaments revealed that keratins form hollow cylinders consisting of multiple protofilaments, with an electron dense core located in the center of the filament. These findings shed light on the complex and remarkable heterogenic architecture of keratin filaments, suggesting that they are highly flexible, dynamic cytoskeletal structures.
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Affiliation(s)
- Miriam S Weber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Matthias Eibauer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Suganya Sivagurunathan
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, United States
| | - Thomas M Magin
- Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, United States
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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11
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Goldman RD, Pederson T. Millie Hughes‐Fulford, 1945‐2021. FASEB J 2021. [DOI: 10.1096/fj.202100305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Robert D. Goldman
- Department of Cell and Developmental BiologyNorthwestern Feinberg School of Medicine Chicago IL USA
| | - Thoru Pederson
- Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA USA
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12
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Kittisopikul M, Shimi T, Tatli M, Tran JR, Zheng Y, Medalia O, Jaqaman K, Adam SA, Goldman RD. Computational analyses reveal spatial relationships between nuclear pore complexes and specific lamins. J Cell Biol 2021; 220:e202007082. [PMID: 33570570 PMCID: PMC7883741 DOI: 10.1083/jcb.202007082] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/15/2020] [Accepted: 01/05/2021] [Indexed: 12/29/2022] Open
Abstract
Nuclear lamin isoforms form fibrous meshworks associated with nuclear pore complexes (NPCs). Using datasets prepared from subpixel and segmentation analyses of 3D-structured illumination microscopy images of WT and lamin isoform knockout mouse embryo fibroblasts, we determined with high precision the spatial association of NPCs with specific lamin isoform fibers. These relationships are retained in the enlarged lamin meshworks of Lmna-/- and Lmnb1-/- fibroblast nuclei. Cryo-ET observations reveal that the lamin filaments composing the fibers contact the nucleoplasmic ring of NPCs. Knockdown of the ring-associated nucleoporin ELYS induces NPC clusters that exclude lamin A/C fibers but include LB1 and LB2 fibers. Knockdown of the nucleoporin TPR or NUP153 alters the arrangement of lamin fibers and NPCs. Evidence that the number of NPCs is regulated by specific lamin isoforms is presented. Overall the results demonstrate that lamin isoforms and nucleoporins act together to maintain the normal organization of lamin meshworks and NPCs within the nuclear envelope.
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Affiliation(s)
- Mark Kittisopikul
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Takeshi Shimi
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
- Cell Biology Center and World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Meltem Tatli
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Joseph Riley Tran
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD
| | - Yixian Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Khuloud Jaqaman
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Stephen A. Adam
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Robert D. Goldman
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
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13
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Tran JR, Paulson DI, Moresco JJ, Adam SA, Yates JR, Goldman RD, Zheng Y. An APEX2 proximity ligation method for mapping interactions with the nuclear lamina. J Cell Biol 2021; 220:e202002129. [PMID: 33306092 PMCID: PMC7737704 DOI: 10.1083/jcb.202002129] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 10/19/2020] [Accepted: 10/29/2020] [Indexed: 01/13/2023] Open
Abstract
The nuclear lamina (NL) is a meshwork found beneath the inner nuclear membrane. The study of the NL is hindered by the insolubility of the meshwork and has driven the development of proximity ligation methods to identify the NL-associated/proximal proteins, RNA, and DNA. To simplify and improve temporal labeling, we fused APEX2 to the NL protein lamin-B1 to map proteins, RNA, and DNA. The identified NL-interacting/proximal RNAs show a long 3' UTR bias, a finding consistent with an observed bias toward longer 3' UTRs in genes deregulated in lamin-null cells. A C-rich motif was identified in these 3' UTR. Our APEX2-based proteomics identifies a C-rich motif binding regulatory protein that exhibits altered localization in lamin-null cells. Finally, we use APEX2 to map lamina-associated domains (LADs) during the cell cycle and uncover short, H3K27me3-rich variable LADs. Thus, the APEX2-based tools presented here permit identification of proteomes, transcriptomes, and genome elements associated with or proximal to the NL.
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Affiliation(s)
- Joseph R. Tran
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
| | - Danielle I. Paulson
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
- Horace Mann School, The Bronx, NY
| | - James J. Moresco
- The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
| | - Stephen A. Adam
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
| | - John R. Yates
- The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
| | - Robert D. Goldman
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
| | - Yixian Zheng
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
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14
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Kittisopikul M, Vahabikashi A, Shimi T, Goldman RD, Jaqaman K. Adaptive multiorientation resolution analysis of complex filamentous network images. Bioinformatics 2020; 36:5093-5103. [PMID: 32653917 DOI: 10.1093/bioinformatics/btaa627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 06/21/2020] [Accepted: 07/03/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Microscopy images of cytoskeletal, nucleoskeletal and other structures contain complex junctions of overlapping filaments with arbitrary geometry. Yet, state-of-the-art algorithms generally perform single orientation analysis to segment these structures, resulting in gaps near junctions, or assume particular junction geometries to detect them. RESULTS We developed a fully automated image analysis approach to address the challenge of determining the number of orientations and their values at each point in space to detect both lines and their junctions. Our approach does not assume any fixed number of orientations or any particular geometry in the case of multiple coincident orientations. It is based on analytically resolving coincident orientations revealed by steerable ridge filtering in an adaptive manner that balances orientation resolution and spatial localization. Combining this multiorientation resolution information with a generalization of the concept of non-maximum suppression allowed us to then identify the centers of lines and their junctions in an image. We validated our approach using a wide array of synthetic junctions and by comparison to manual segmentation. We also applied it to light microscopy images of cytoskeletal and nucleoskeletal networks. AVAILABILITY AND IMPLEMENTATION https://github.com/mkitti/AdaptiveResolutionOrientationSpace. SUPPLEMENTARY INFORMATION Supplementary information is available at Bioinformatics online.
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Affiliation(s)
- Mark Kittisopikul
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Amir Vahabikashi
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Takeshi Shimi
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- World Research Hub Initiative Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Khuloud Jaqaman
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
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15
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Patteson AE, Vahabikashi A, Goldman RD, Janmey PA. BioEssays 11/2020. Bioessays 2020. [DOI: 10.1002/bies.202070113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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16
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Patteson AE, Vahabikashi A, Goldman RD, Janmey PA. Mechanical and Non-Mechanical Functions of Filamentous and Non-Filamentous Vimentin. Bioessays 2020; 42:e2000078. [PMID: 32893352 PMCID: PMC8349470 DOI: 10.1002/bies.202000078] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 08/04/2020] [Indexed: 12/20/2022]
Abstract
Intermediate filaments (IFs) formed by vimentin are less understood than their cytoskeletal partners, microtubules and F-actin, but the unique physical properties of IFs, especially their resistance to large deformations, initially suggest a mechanical function. Indeed, vimentin IFs help regulate cell mechanics and contractility, and in crowded 3D environments they protect the nucleus during cell migration. Recently, a multitude of studies, often using genetic or proteomic screenings show that vimentin has many non-mechanical functions within and outside of cells. These include signaling roles in wound healing, lipogenesis, sterol processing, and various functions related to extracellular and cell surface vimentin. Extracellular vimentin is implicated in marking circulating tumor cells, promoting neural repair, and mediating the invasion of host cells by viruses, including SARS-CoV, or bacteria such as Listeria and Streptococcus. These findings underscore the fundamental role of vimentin in not only cell mechanics but also a range of physiological functions. Also see the video abstract here https://youtu.be/YPfoddqvz-g.
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Affiliation(s)
- Alison E Patteson
- Physics Department, Syracuse University, Syracuse, NY 13244
- BioInspired Institute, Syracuse University, Syracuse, NY 13244
| | - Amir Vahabikashi
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago IL 60611
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago IL 60611
| | - Paul A. Janmey
- Institute for Medicine and Engineering, Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104
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17
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Wu H, Shen Y, Wang D, Herrmann H, Goldman RD, Weitz DA. Effect of Divalent Cations on the Structure and Mechanics of Vimentin Intermediate Filaments. Biophys J 2020; 119:55-64. [PMID: 32521238 DOI: 10.1016/j.bpj.2020.05.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 12/30/2022] Open
Abstract
Divalent cations behave as effective cross-linkers of intermediate filaments (IFs) such as vimentin IF (VIF). These interactions have been mostly attributed to their multivalency. However, ion-protein interactions often depend on the ion species, and these effects have not been widely studied in IFs. Here, we investigate the effects of two biologically important divalent cations, Zn2+ and Ca2+, on VIF network structure and mechanics in vitro. We find that the network structure is unperturbed at micromolar Zn2+ concentrations, but strong bundle formation is observed at a concentration of 100 μM. Microrheological measurements show that network stiffness increases with cation concentration. However, bundling of filaments softens the network. This trend also holds for VIF networks formed in the presence of Ca2+, but remarkably, a concentration of Ca2+ that is two orders higher is needed to achieve the same effect as with Zn2+, which suggests the importance of salt-protein interactions as described by the Hofmeister effect. Furthermore, we find evidence of competitive binding between the two divalent ion species. Hence, specific interactions between VIFs and divalent cations are likely to be an important mechanism by which cells can control their cytoplasmic mechanics.
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Affiliation(s)
- Huayin Wu
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts
| | - Yinan Shen
- Department of Physics, Harvard University, Cambridge, Massachusetts
| | - Dianzhuo Wang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Harald Herrmann
- Division of Cell Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Neuropathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts; Department of Physics, Harvard University, Cambridge, Massachusetts.
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18
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Goldman RD. In Memoriam: Gerald Weissmann, MD. FASEB J 2020; 33:10594-10595. [PMID: 32092232 DOI: 10.1096/fj.191002ufm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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19
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Patteson AE, Vahabikashi A, Pogoda K, Adam SA, Mandal K, Kittisopikul M, Sivagurunathan S, Goldman A, Goldman RD, Janmey PA. Vimentin protects cells against nuclear rupture and DNA damage during migration. J Cell Biol 2019; 218:4079-4092. [PMID: 31676718 PMCID: PMC6891099 DOI: 10.1083/jcb.201902046] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/12/2019] [Accepted: 09/18/2019] [Indexed: 01/30/2023] Open
Abstract
Mammalian cells frequently migrate through tight spaces during normal embryogenesis, wound healing, diapedesis, or in pathological situations such as metastasis. Nuclear size and shape are important factors in regulating the mechanical properties of cells during their migration through such tight spaces. At the onset of migratory behavior, cells often initiate the expression of vimentin, an intermediate filament protein that polymerizes into networks extending from a juxtanuclear cage to the cell periphery. However, the role of vimentin intermediate filaments (VIFs) in regulating nuclear shape and mechanics remains unknown. Here, we use wild-type and vimentin-null mouse embryonic fibroblasts to show that VIFs regulate nuclear shape and perinuclear stiffness, cell motility in 3D, and the ability of cells to resist large deformations. These changes increase nuclear rupture and activation of DNA damage repair mechanisms, which are rescued by exogenous reexpression of vimentin. Our findings show that VIFs provide mechanical support to protect the nucleus and genome during migration.
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Affiliation(s)
- Alison E Patteson
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA.,Physics Department, Syracuse University, Syracuse, NY
| | - Amir Vahabikashi
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago IL
| | - Katarzyna Pogoda
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA.,Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago IL
| | - Kalpana Mandal
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA
| | - Mark Kittisopikul
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago IL
| | - Suganya Sivagurunathan
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago IL
| | - Anne Goldman
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago IL
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago IL
| | - Paul A Janmey
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA .,Department of Physiology, University of Pennsylvania, Philadelphia, PA
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20
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Stephens AD, Liu PZ, Kandula V, Chen H, Almassalha LM, Herman C, Backman V, O’Halloran T, Adam SA, Goldman RD, Banigan EJ, Marko JF. Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation. Mol Biol Cell 2019; 30:2320-2330. [PMID: 31365328 PMCID: PMC6743459 DOI: 10.1091/mbc.e19-05-0286] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
The nucleus houses, organizes, and protects chromatin to ensure genome integrity and proper gene expression, but how the nucleus adapts mechanically to changes in the extracellular environment is poorly understood. Recent studies have revealed that extracellular physical stresses induce chromatin compaction via mechanotransductive processes. We report that increased extracellular multivalent cations lead to increased heterochromatin levels through activation of mechanosensitive ion channels (MSCs), without large-scale cell stretching. In cells with perturbed chromatin or lamins, this increase in heterochromatin suppresses nuclear blebbing associated with nuclear rupture and DNA damage. Through micromanipulation force measurements, we show that this increase in heterochromatin increases chromatin-based nuclear rigidity, which protects nuclear morphology and function. In addition, transduction of elevated extracellular cations rescues nuclear morphology in model and patient cells of human diseases, including progeria and the breast cancer model cell line MDA-MB-231. We conclude that nuclear mechanics, morphology, and function can be modulated by cell sensing of the extracellular environment through MSCs and consequent changes to histone modification state and chromatin-based nuclear rigidity.
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Affiliation(s)
- Andrew D. Stephens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Patrick Z. Liu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Viswajit Kandula
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Haimei Chen
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Luay M. Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208
| | - Cameron Herman
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208
| | - Thomas O’Halloran
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Stephen A. Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Robert D. Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Edward J. Banigan
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - John F. Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208
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21
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Stephens AD, Liu PZ, Kandula V, Chen H, Almassalha LM, Herman C, Backman V, O'Halloran T, Adam SA, Goldman RD, Banigan EJ, Marko JF. Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation. Mol Biol Cell 2019:mbcE19050286T. [PMID: 31216230 DOI: 10.1091/mbc.e19-05-0286-t] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The nucleus houses, organizes, and protects chromatin to ensure genome integrity and proper gene expression, but how the nucleus adapts mechanically to changes in the extracellular environment is poorly understood. Recent studies have revealed that extracellular physical stresses induce chromatin compaction via mechanotransductive processes. We report that increased extracellular multivalent cations lead to increased heterochromatin levels through activation of mechanosensitive ion channels, without large-scale cell stretching. In cells with perturbed chromatin or lamins, this increase in heterochromatin suppresses nuclear blebbing associated with nuclear rupture and DNA damage. Through micromanipulation force measurements, we show that this increase in heterochromatin increases chromatin-based nuclear rigidity, which protects nuclear morphology and function. In addition, transduction of elevated extracellular cations rescues nuclear morphology in model and patient cells of human diseases, including progeria and the breast cancer model cell line MDA-MB-231. We conclude that nuclear mechanics, morphology, and function can be modulated by cell sensing of the extracellular environment through mechanosensitive ion channels and consequent changes to histone modification state and chromatin-based nuclear rigidity.
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Affiliation(s)
- Andrew D Stephens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Patrick Z Liu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Viswajit Kandula
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Haimei Chen
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Luay M Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208
| | - Cameron Herman
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208
| | - Thomas O'Halloran
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Edward J Banigan
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208
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22
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Kittisopikul M, Virtanen L, Taimen P, Goldman RD. Quantitative Analysis of Nuclear Lamins Imaged by Super-Resolution Light Microscopy. Cells 2019; 8:E361. [PMID: 31003483 PMCID: PMC6524165 DOI: 10.3390/cells8040361] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/13/2019] [Accepted: 04/14/2019] [Indexed: 11/20/2022] Open
Abstract
The nuclear lamina consists of a dense fibrous meshwork of nuclear lamins, Type V intermediate filaments, and is ~14 nm thick according to recent cryo-electron tomography studies. Recent advances in light microscopy have extended the resolution to a scale allowing for the fine structure of the lamina to be imaged in the context of the whole nucleus. We review quantitative approaches to analyze the imaging data of the nuclear lamina as acquired by structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM), as well as the requisite cell preparation techniques. In particular, we discuss the application of steerable filters and graph-based methods to segment the structure of the four mammalian lamin isoforms (A, C, B1, and B2) and extract quantitative information.
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Affiliation(s)
- Mark Kittisopikul
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Laura Virtanen
- Institute of Biomedicine, Research Center for Cancer, Infections and Immunity, University of Turku, 20520 Turku, Finland.
| | - Pekka Taimen
- Institute of Biomedicine, Research Center for Cancer, Infections and Immunity, University of Turku, 20520 Turku, Finland.
- Department of Pathology, Turku University Hospital, 20520 Turku, Finland.
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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23
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Butin-Israeli V, Bui TM, Wiesolek HL, Mascarenhas L, Lee JJ, Mehl LC, Knutson KR, Adam SA, Goldman RD, Beyder A, Wiesmuller L, Hanauer SB, Sumagin R. Neutrophil-induced genomic instability impedes resolution of inflammation and wound healing. J Clin Invest 2019; 129:712-726. [PMID: 30640176 DOI: 10.1172/jci122085] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022] Open
Abstract
Neutrophil (PMN) infiltration of the intestinal mucosa is a hallmark of tissue injury associated with inflammatory bowel diseases (IBDs). The pathological effects of PMNs are largely attributed to the release of soluble mediators and reactive oxygen species (ROS). We identified what we believe is a new, ROS-independent mechanism whereby activated tissue-infiltrating PMNs release microparticles armed with proinflammatory microRNAs (miR-23a and miR-155). Using IBD clinical samples, and in vitro and in vivo injury models, we show that PMN-derived miR-23a and miR-155 promote accumulation of double-strand breaks (DSBs) by inducing lamin B1-dependent replication fork collapse and inhibition of homologous recombination (HR) by targeting HR-regulator RAD51. DSB accumulation in injured epithelium led to impaired colonic healing and genomic instability. Targeted inhibition of miR-23a and miR-155 in cultured intestinal epithelial cells and in acutely injured mucosa decreased the detrimental effects of PMNs and enhanced tissue healing responses, suggesting that this approach can be used in therapies aimed at resolution of inflammation, in wound healing, and potentially to prevent neoplasia.
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Affiliation(s)
- Veronika Butin-Israeli
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Triet M Bui
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Hannah L Wiesolek
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lorraine Mascarenhas
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joseph J Lee
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lindsey C Mehl
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kaitlyn R Knutson
- Enteric Neuroscience Program, Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Arthur Beyder
- Enteric Neuroscience Program, Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota, USA.,Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Lisa Wiesmuller
- Department of Obstetrics and Gynecology, Ulm University, Ulm, Germany
| | | | - Ronen Sumagin
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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24
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Vahabikashi A, Park CY, Perkumas K, Zhang Z, Deurloo EK, Wu H, Weitz DA, Stamer WD, Goldman RD, Fredberg JJ, Johnson M. Probe Sensitivity to Cortical versus Intracellular Cytoskeletal Network Stiffness. Biophys J 2019; 116:518-529. [PMID: 30685055 DOI: 10.1016/j.bpj.2018.12.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/04/2018] [Accepted: 12/20/2018] [Indexed: 11/19/2022] Open
Abstract
In development, wound healing, and pathology, cell biomechanical properties are increasingly recognized as being of central importance. To measure these properties, experimental probes of various types have been developed, but how each probe reflects the properties of heterogeneous cell regions has remained obscure. To better understand differences attributable to the probe technology, as well as to define the relative sensitivity of each probe to different cellular structures, here we took a comprehensive approach. We studied two cell types-Schlemm's canal endothelial cells and mouse embryonic fibroblasts (MEFs)-using four different probe technologies: 1) atomic force microscopy (AFM) with sharp tip, 2) AFM with round tip, 3) optical magnetic twisting cytometry (OMTC), and 4) traction microscopy (TM). Perturbation of Schlemm's canal cells with dexamethasone treatment, α-actinin overexpression, or RhoA overexpression caused increases in traction reported by TM and stiffness reported by sharp-tip AFM as compared to corresponding controls. By contrast, under these same experimental conditions, stiffness reported by round-tip AFM and by OMTC indicated little change. Knockout (KO) of vimentin in MEFs caused a diminution of traction reported by TM, as well as stiffness reported by sharp-tip and round-tip AFM. However, stiffness reported by OMTC in vimentin-KO MEFs was greater than in wild type. Finite-element analysis demonstrated that this paradoxical OMTC result in vimentin-KO MEFs could be attributed to reduced cell thickness. Our results also suggest that vimentin contributes not only to intracellular network stiffness but also cortex stiffness. Taken together, this evidence suggests that AFM sharp tip and TM emphasize properties of the actin-rich shell of the cell, whereas round-tip AFM and OMTC emphasize those of the noncortical intracellular network.
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Affiliation(s)
- Amir Vahabikashi
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois
| | - Chan Young Park
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Kristin Perkumas
- Department of Ophthalmology, Duke University, Durham, North Carolina
| | - Zhiguo Zhang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Emily K Deurloo
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Huayin Wu
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts
| | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts; Department of Physics, Harvard University, Cambridge, Massachusetts
| | - W Daniel Stamer
- Department of Ophthalmology, Duke University, Durham, North Carolina; Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jeffrey J Fredberg
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Mark Johnson
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois; Department of Ophthalmology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Department of Mechanical Engineering, Northwestern University, Evanston, Illinois.
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25
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Abstract
Organisms in the three domains of life depend on protein polymers to form a cytoskeleton that helps to establish their shapes, maintain their mechanical integrity, divide, and, in many cases, move. Eukaryotes have the most complex cytoskeletons, comprising three cytoskeletal polymers-actin filaments, intermediate filaments, and microtubules-acted on by three families of motor proteins (myosin, kinesin, and dynein). Prokaryotes have polymers of proteins homologous to actin and tubulin but no motors, and a few bacteria have a protein related to intermediate filament proteins.
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Affiliation(s)
- Thomas D Pollard
- Departments of Molecular Cellular and Developmental Biology, Molecular Biophysics and Biochemistry, and Cell Biology, Yale University, New Haven, Connecticut 06520-8103
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
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26
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Robert A, Tian P, Adam SA, Kittisopikul M, Jaqaman K, Goldman RD, Gelfand VI. Kinesin-dependent transport of keratin filaments: a unified mechanism for intermediate filament transport. FASEB J 2018; 33:388-399. [PMID: 29944446 PMCID: PMC6355078 DOI: 10.1096/fj.201800604r] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Keratin intermediate filaments (IFs) are the major cytoskeletal component in epithelial cells. The dynamics of keratin IFs have been described to depend mostly on the actin cytoskeleton, but the rapid transport of fully polymerized keratin filaments has not been reported. In this work, we used a combination of photoconversion experiments and clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated protein 9 genome editing to study the role of microtubules and microtubule motors in keratin filament transport. We found that long keratin filaments, like other types of IFs, are transported along microtubules by kinesin-1. Our data revealed that keratin and vimentin are nonconventional kinesin-1 cargoes because their transport did not require kinesin light chains, which are a typical adapter for kinesin-dependent cargo transport. Furthermore, we found that the same domain of the kinesin heavy chain tail is involved in keratin and vimentin IF transport, strongly suggesting that multiple types of IFs move along microtubules using an identical mechanism.-Robert, A., Tian, P., Adam, S. A., Kittisopikul, M., Jaqaman, K., Goldman, R. D., Gelfand, V. I. Kinesin-dependent transport of keratin filaments: a unified mechanism for intermediate filament transport.
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Affiliation(s)
- Amélie Robert
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Peirun Tian
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Mark Kittisopikul
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA; and
| | - Khuloud Jaqaman
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA; and.,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Vladimir I Gelfand
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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27
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Wang Z, Divanyan A, Jourd'heuil FL, Goldman RD, Ridge KM, Jourd'heuil D, Lopez-Soler RI. Vimentin expression is required for the development of EMT-related renal fibrosis following unilateral ureteral obstruction in mice. Am J Physiol Renal Physiol 2018; 315:F769-F780. [PMID: 29631355 DOI: 10.1152/ajprenal.00340.2017] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Most renal transplants ultimately fail secondary to chronic allograft nephropathy (CAN). Vimentin (vim) is a member of the intermediate filament family of proteins and has been shown to be important in the development of CAN. One of the pathways leading to chronic renal fibrosis after transplant is thought to be epithelial to mesenchymal transition (EMT). Even though vim expression is one of the main steps of EMT, it is unknown whether vim expression is required for EMT leading to renal fibrosis and allograft loss. To this end, the role of vim in renal fibrosis was determined via unilateral ureteral obstruction (UUO) in vim knockout mice (129 svs6 vim -/-). Following UUO, kidneys were recovered and analyzed via Western blotting, immunofluorescence, and transcriptomics. Cultured human proximal renal tubular (HK-2) cells were subjected to lentiviral-driven inhibition of vim expression and then treated with transforming growth factor (TGF)-β to undergo EMT. Immunoblotting as well as wound healing assays were used to determine development of EMT. Western blotting analyses of mice undergoing UUO reveal increased levels of vim soon after UUO. As expected, interstitial collagen deposition increased in control mice following UUO but decreased in vim -/- kidneys. Immunofluorescence analyses also revealed altered localization of β-catenin in vim -/- mice undergoing UUO without significant changes in mRNA levels. However, RNA sequencing revealed a decrease in β-catenin-dependent genes in vim -/- kidneys. Finally, vim-silenced HK-2 cell lines undergoing EMT were shown to have decreased cellular migration during wound healing. We conclude that vim inhibition decreases fibrosis following UUO by possibly altering β-catenin localization and downstream signaling.
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Affiliation(s)
- Zheng Wang
- Department of Molecular and Cellular Physiology, Albany Medical College , Albany, New York
| | - Alex Divanyan
- Department of Molecular and Cellular Physiology, Albany Medical College , Albany, New York
| | - Frances L Jourd'heuil
- Department of Molecular and Cellular Physiology, Albany Medical College , Albany, New York
| | - Robert D Goldman
- Department of Cellular and Molecular Biology, Northwestern University , Chicago, Illinois
| | - Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Northwestern University , Chicago, Illinois
| | - David Jourd'heuil
- Department of Molecular and Cellular Physiology, Albany Medical College , Albany, New York
| | - Reynold I Lopez-Soler
- Division of Surgery, Section of Transplantation, Albany Medical Center , Albany, New York
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28
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Stephens AD, Liu PZ, Banigan EJ, Almassalha LM, Backman V, Adam SA, Goldman RD, Marko JF. Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins. Mol Biol Cell 2018; 29:220-233. [PMID: 29142071 PMCID: PMC5909933 DOI: 10.1091/mbc.e17-06-0410] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/17/2017] [Accepted: 11/08/2017] [Indexed: 01/29/2023] Open
Abstract
Nuclear shape and architecture influence gene localization, mechanotransduction, transcription, and cell function. Abnormal nuclear morphology and protrusions termed "blebs" are diagnostic markers for many human afflictions including heart disease, aging, progeria, and cancer. Nuclear blebs are associated with both lamin and chromatin alterations. A number of prior studies suggest that lamins dictate nuclear morphology, but the contributions of altered chromatin compaction remain unclear. We show that chromatin histone modification state dictates nuclear rigidity, and modulating it is sufficient to both induce and suppress nuclear blebs. Treatment of mammalian cells with histone deacetylase inhibitors to increase euchromatin or histone methyltransferase inhibitors to decrease heterochromatin results in a softer nucleus and nuclear blebbing, without perturbing lamins. Conversely, treatment with histone demethylase inhibitors increases heterochromatin and chromatin nuclear rigidity, which results in reduced nuclear blebbing in lamin B1 null nuclei. Notably, increased heterochromatin also rescues nuclear morphology in a model cell line for the accelerated aging disease Hutchinson-Gilford progeria syndrome caused by mutant lamin A, as well as cells from patients with the disease. Thus, chromatin histone modification state is a major determinant of nuclear blebbing and morphology via its contribution to nuclear rigidity.
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Affiliation(s)
- Andrew D Stephens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Patrick Z Liu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Edward J Banigan
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Luay M Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208.,Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208
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29
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Soomro A, Alsop RJ, Negishi A, Kreplak L, Fudge D, Kuczmarski ER, Goldman RD, Rheinstädter MC. Giant axonal neuropathy alters the structure of keratin intermediate filaments in human hair. J R Soc Interface 2017; 14:rsif.2017.0123. [PMID: 28424304 DOI: 10.1098/rsif.2017.0123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 03/24/2017] [Indexed: 11/12/2022] Open
Abstract
Giant axonal neuropathy (GAN) follows an autosomal recessive genetic inheritance and impedes the peripheral and central nervous system due to axonal swellings that are packed with neurofilaments. The patients display a number of phenotypes, including hypotonia, muscle weakness, decreased reflexes, ataxia, seizures, intellectual disability, pale skin and often curled hair. We used X-ray diffraction and tensile testing to determine potential changes to the structure of keratin intermediate filaments (IFs) in the hair of patients with GAN. A statistically significant decrease in the 47 and the 27 Å diffraction signals were observed. Tensile tests determined that the hair was slightly stiffer, stronger and more extensible in GAN patients. These results suggest that the structure of keratin IFs in hair is altered in GAN, and the findings are compatible with an increased positional disorder of the keratin tetramers within the hair fibres.
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Affiliation(s)
- Asfia Soomro
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
| | - Richard J Alsop
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
| | - Atsuko Negishi
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Laurent Kreplak
- Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Douglas Fudge
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Edward R Kuczmarski
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL, USA
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL, USA
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30
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Liu PZ, Stephens AD, Banigan EJ, Almassalha L, Backman V, Adams SA, Goldman RD, Marko JF. Nuclear Blebbing Solely as a Function of Chromatin Compaction State. FASEB J 2017. [DOI: 10.1096/fasebj.31.1_supplement.lb237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Patrick Z. Liu
- Department of Molecular BiosciencesNorthwestern UniversityEvanstonIL
| | | | - Edward J. Banigan
- Department of Physics and AstronomyNorthwestern UniversityEvanstonIL
| | - Luay Almassalha
- Department of Biomedical EngineeringNorthwestern UniversityEvanstonIL
| | - Vadim Backman
- Department of Biomedical EngineeringNorthwestern UniversityEvanstonIL
| | - Stephen A. Adams
- Department of Cell and Molecular BiologyFeinberg School of Medicine Northwestern UniversityChicagoIL
| | - Robert D. Goldman
- Department of Cell and Molecular BiologyFeinberg School of Medicine Northwestern UniversityChicagoIL
| | - John F. Marko
- Department of Molecular BiosciencesNorthwestern UniversityEvanstonIL
- Department of Physics and AstronomyNorthwestern UniversityEvanstonIL
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31
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Turgay Y, Eibauer M, Goldman AE, Shimi T, Khayat M, Ben-Harush K, Dubrovsky-Gaupp A, Sapra KT, Goldman RD, Medalia O. The molecular architecture of lamins in somatic cells. Nature 2017; 543:261-264. [PMID: 28241138 DOI: 10.1038/nature21382] [Citation(s) in RCA: 269] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 01/11/2017] [Indexed: 01/13/2023]
Abstract
The nuclear lamina is a fundamental constituent of metazoan nuclei. It is composed mainly of lamins, which are intermediate filament proteins that assemble into a filamentous meshwork, bridging the nuclear envelope and chromatin. Besides providing structural stability to the nucleus, the lamina is involved in many nuclear activities, including chromatin organization, transcription and replication. However, the structural organization of the nuclear lamina is poorly understood. Here we use cryo-electron tomography to obtain a detailed view of the organization of the lamin meshwork within the lamina. Data analysis of individual lamin filaments resolves a globular-decorated fibre appearance and shows that A- and B-type lamins assemble into tetrameric filaments of 3.5 nm thickness. Thus, lamins exhibit a structure that is remarkably different from the other canonical cytoskeletal elements. Our findings define the architecture of the nuclear lamin meshworks at molecular resolution, providing insights into their role in scaffolding the nuclear lamina.
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Affiliation(s)
- Yagmur Turgay
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matthias Eibauer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anne E Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, Illinois 60611, USA
| | - Takeshi Shimi
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, Illinois 60611, USA
| | - Maayan Khayat
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, 84105 Beer-Sheva, Israel
| | - Kfir Ben-Harush
- Department of Chemical Engineering, Shamoon College of Engineering, Jabotinsky 84, 77245 Ashdod, Israel
| | - Anna Dubrovsky-Gaupp
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - K Tanuj Sapra
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, 303 E Chicago Avenue, Chicago, Illinois 60611, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, 84105 Beer-Sheva, Israel
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32
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Stephens AD, Banigan EJ, Adam SA, Goldman RD, Marko JF. Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus. Mol Biol Cell 2017; 28:1984-1996. [PMID: 28057760 PMCID: PMC5541848 DOI: 10.1091/mbc.e16-09-0653] [Citation(s) in RCA: 267] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/04/2016] [Accepted: 12/29/2016] [Indexed: 02/02/2023] Open
Abstract
The cell nucleus must continually resist and respond to intercellular and intracellular mechanical forces to transduce mechanical signals and maintain proper genome organization and expression. Altered nuclear mechanics is associated with many human diseases, including heart disease, progeria, and cancer. Chromatin and nuclear envelope A-type lamin proteins are known to be key nuclear mechanical components perturbed in these diseases, but their distinct mechanical contributions are not known. Here we directly establish the separate roles of chromatin and lamin A/C and show that they determine two distinct mechanical regimes via micromanipulation of single isolated nuclei. Chromatin governs response to small extensions (<3 μm), and euchromatin/heterochromatin levels modulate the stiffness. In contrast, lamin A/C levels control nuclear strain stiffening at large extensions. These results can be understood through simulations of a polymeric shell and cross-linked polymer interior. Our results provide a framework for understanding the differential effects of chromatin and lamin A/C in cell nuclear mechanics and their alterations in disease.
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Affiliation(s)
- Andrew D Stephens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Edward J Banigan
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208.,Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208
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33
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Gan Z, Ding L, Burckhardt CJ, Lowery J, Zaritsky A, Sitterley K, Mota A, Costigliola N, Starker CG, Voytas DF, Tytell J, Goldman RD, Danuser G. Vimentin Intermediate Filaments Template Microtubule Networks to Enhance Persistence in Cell Polarity and Directed Migration. Cell Syst 2016; 3:500-501. [PMID: 27883892 DOI: 10.1016/j.cels.2016.11.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Lin NH, Huang YS, Opal P, Goldman RD, Messing A, Perng MD. The role of gigaxonin in the degradation of the glial-specific intermediate filament protein GFAP. Mol Biol Cell 2016; 27:3980-3990. [PMID: 27798231 PMCID: PMC5156539 DOI: 10.1091/mbc.e16-06-0362] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/03/2016] [Accepted: 10/19/2016] [Indexed: 01/04/2023] Open
Abstract
Alexander disease (AxD) is a primary genetic disorder of astrocytes caused by dominant mutations in the gene encoding the intermediate filament (IF) protein GFAP. This disease is characterized by excessive accumulation of GFAP, known as Rosenthal fibers, within astrocytes. Abnormal GFAP aggregation also occurs in giant axon neuropathy (GAN), which is caused by recessive mutations in the gene encoding gigaxonin. Given that one of the functions of gigaxonin is to facilitate proteasomal degradation of several IF proteins, we sought to determine whether gigaxonin is involved in the degradation of GFAP. Using a lentiviral transduction system, we demonstrated that gigaxonin levels influence the degradation of GFAP in primary astrocytes and in cell lines that express this IF protein. Gigaxonin was similarly involved in the degradation of some but not all AxD-associated GFAP mutants. In addition, gigaxonin directly bound to GFAP, and inhibition of proteasome reversed the clearance of GFAP in cells achieved by overexpressing gigaxonin. These studies identify gigaxonin as an important factor that targets GFAP for degradation through the proteasome pathway. Our findings provide a critical foundation for future studies aimed at reducing or reversing pathological accumulation of GFAP as a potential therapeutic strategy for AxD and related diseases.
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Affiliation(s)
- Ni-Hsuan Lin
- Institute of Molecular Medicine, College of Life Sciences, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yu-Shan Huang
- Institute of Molecular Medicine, College of Life Sciences, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Puneet Opal
- Davee Department of Neurology, Northwestern University, Chicago, IL 60611.,Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Albee Messing
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705.,Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53705
| | - Ming-Der Perng
- Institute of Molecular Medicine, College of Life Sciences, National Tsing Hua University, Hsinchu 300, Taiwan
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35
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Gan Z, Ding L, Burckhardt CJ, Lowery J, Zaritsky A, Sitterley K, Mota A, Costigliola N, Starker CG, Voytas DF, Tytell J, Goldman RD, Danuser G. Vimentin Intermediate Filaments Template Microtubule Networks to Enhance Persistence in Cell Polarity and Directed Migration. Cell Syst 2016; 3:252-263.e8. [PMID: 27667364 DOI: 10.1016/j.cels.2016.08.007] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/01/2016] [Accepted: 08/05/2016] [Indexed: 10/24/2022]
Abstract
Increased expression of vimentin intermediate filaments (VIFs) enhances directed cell migration, but the mechanism behind VIFs' effect on motility is not understood. VIFs interact with microtubules, whose organization contributes to polarity maintenance in migrating cells. Here, we characterize the dynamic coordination of VIF and microtubule networks in wounded monolayers of retinal pigment epithelial cells. By genome editing, we fluorescently labeled endogenous vimentin and α-tubulin, and we developed computational image analysis to delineate architecture and interactions of the two networks. Our results show that VIFs assemble an ultrastructural copy of the previously polarized microtubule network. Because the VIF network is long-lived compared to the microtubule network, VIFs template future microtubule growth along previous microtubule tracks, thus providing a feedback mechanism that maintains cell polarity. VIF knockdown prevents cells from polarizing and migrating properly during wound healing. We suggest that VIFs' templating function establishes a memory in microtubule organization that enhances persistence in cell polarization in general and migration in particular.
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Affiliation(s)
- Zhuo Gan
- Department of Cell Biology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75235, USA
| | - Liya Ding
- Department of Cell Biology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75235, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christoph J Burckhardt
- Department of Cell Biology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75235, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Lowery
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Evanston, IL 60208, USA
| | - Assaf Zaritsky
- Department of Cell Biology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75235, USA
| | | | - Andressa Mota
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nancy Costigliola
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Colby G Starker
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jessica Tytell
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Evanston, IL 60208, USA
| | - Gaudenz Danuser
- Department of Cell Biology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75235, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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36
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West G, Gullmets J, Virtanen L, Li SP, Keinänen A, Shimi T, Mauermann M, Heliö T, Kaartinen M, Ollila L, Kuusisto J, Eriksson JE, Goldman RD, Herrmann H, Taimen P. Deleterious assembly of the lamin A/C mutant p.S143P causes ER stress in familial dilated cardiomyopathy. J Cell Sci 2016; 129:2732-43. [PMID: 27235420 DOI: 10.1242/jcs.184150] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/20/2016] [Indexed: 01/12/2023] Open
Abstract
Mutation of the LMNA gene, encoding nuclear lamin A and lamin C (hereafter lamin A/C), is a common cause of familial dilated cardiomyopathy (DCM). Among Finnish DCM patients, the founder mutation c.427T>C (p.S143P) is the most frequently reported genetic variant. Here, we show that p.S143P lamin A/C is more nucleoplasmic and soluble than wild-type lamin A/C and accumulates into large intranuclear aggregates in a fraction of cultured patient fibroblasts as well as in cells ectopically expressing either FLAG- or GFP-tagged p.S143P lamin A. In fluorescence loss in photobleaching (FLIP) experiments, non-aggregated EGFP-tagged p.S143P lamin A was significantly more dynamic. In in vitro association studies, p.S143P lamin A failed to form appropriate filament structures but instead assembled into disorganized aggregates similar to those observed in patient cell nuclei. A whole-genome expression analysis revealed an elevated unfolded protein response (UPR) in cells expressing p.S143P lamin A/C. Additional endoplasmic reticulum (ER) stress induced by tunicamycin reduced the viability of cells expressing mutant lamin further. In summary, p.S143P lamin A/C affects normal lamina structure and influences the cellular stress response, homeostasis and viability.
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Affiliation(s)
- Gun West
- Department of Pathology, University of Turku and Turku University Hospital, 20520 Turku, Finland MediCity Research Laboratory, 20520 Turku, Finland
| | - Josef Gullmets
- Department of Pathology, University of Turku and Turku University Hospital, 20520 Turku, Finland MediCity Research Laboratory, 20520 Turku, Finland Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Laura Virtanen
- Department of Pathology, University of Turku and Turku University Hospital, 20520 Turku, Finland MediCity Research Laboratory, 20520 Turku, Finland
| | - Song-Ping Li
- Department of Pathology, University of Turku and Turku University Hospital, 20520 Turku, Finland MediCity Research Laboratory, 20520 Turku, Finland
| | - Anni Keinänen
- Department of Pathology, University of Turku and Turku University Hospital, 20520 Turku, Finland MediCity Research Laboratory, 20520 Turku, Finland
| | - Takeshi Shimi
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Monika Mauermann
- Division of Molecular Genetics, German Cancer Research Center, 69120 Heidelberg, Germany Institute of Neuropathology, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Tiina Heliö
- Heart and Lung Center Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
| | - Maija Kaartinen
- Heart and Lung Center Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
| | - Laura Ollila
- Heart and Lung Center Helsinki University Hospital and University of Helsinki, 00029 Helsinki, Finland
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - John E Eriksson
- Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Robert D Goldman
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Harald Herrmann
- Division of Molecular Genetics, German Cancer Research Center, 69120 Heidelberg, Germany Institute of Neuropathology, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Pekka Taimen
- Department of Pathology, University of Turku and Turku University Hospital, 20520 Turku, Finland MediCity Research Laboratory, 20520 Turku, Finland
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Israeli E, Dryanovski DI, Schumacker PT, Chandel NS, Singer JD, Julien JP, Goldman RD, Opal P. Intermediate filament aggregates cause mitochondrial dysmotility and increase energy demands in giant axonal neuropathy. Hum Mol Genet 2016; 25:2143-2157. [PMID: 27000625 DOI: 10.1093/hmg/ddw081] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/07/2016] [Indexed: 12/26/2022] Open
Abstract
Intermediate filaments (IFs) are cytoskeletal polymers that extend from the nucleus to the cell membrane, giving cells their shape and form. Abnormal accumulation of IFs is involved in the pathogenesis of number neurodegenerative diseases, but none as clearly as giant axonal neuropathy (GAN), a ravaging disease caused by mutations in GAN, encoding gigaxonin. Patients display early and severe degeneration of the peripheral nervous system along with IF accumulation, but it has been difficult to link GAN mutations to any particular dysfunction, in part because GAN null mice have a very mild phenotype. We therefore established a robust dorsal root ganglion neuronal model that mirrors key cellular events underlying GAN. We demonstrate that gigaxonin is crucial for ubiquitin-proteasomal degradation of neuronal IF. Moreover, IF accumulation impairs mitochondrial motility and is associated with metabolic and oxidative stress. These results have implications for other neurological disorders whose pathology includes IF accumulation.
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Affiliation(s)
| | | | | | - Navdeep S Chandel
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jeffrey D Singer
- Department of Biology, Portland State University, Portland, OR, USA and
| | - Jean P Julien
- Research Centre of IUSMQ, Department of Psychiatry and Neuroscience of Laval University, Quebec, QC, G1V 0A6, Canada
| | | | - Puneet Opal
- Davee Department of Neurology, Department of Cell and Molecular Biology,
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Takeshi S, Pack CG, Goldman RD. Analyses of the Dynamic Properties of Nuclear Lamins by Fluorescence Recovery After Photobleaching (FRAP) and Fluorescence Correlation Spectroscopy (FCS). Methods Mol Biol 2016; 1411:99-111. [PMID: 27147036 DOI: 10.1007/978-1-4939-3530-7_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The major structural components of the nuclear lamina are the A- and B-type nuclear lamin proteins which are also present in the nucleoplasm. Studies of molecular movements of the lamins in both the lamina and nucleoplasm of living cell nuclei have provided insights into their roles in maintaining nuclear architecture. In this chapter, we present protocols for quantitatively measuring the mobilities of lamin proteins by fluorescence recovery after photobleaching (FRAP) and fluorescence correlation spectroscopy (FCS) in mammalian cell nuclei.
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Affiliation(s)
- Shimi Takeshi
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave., Chicago, IL, 60611, USA.,Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Chan-Gi Pack
- ASAN Institute for Life Sciences, ASAN Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave., Chicago, IL, 60611, USA.
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39
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Lowery J, Jain N, Kuczmarski ER, Mahammad S, Goldman A, Gelfand VI, Opal P, Goldman RD. Abnormal intermediate filament organization alters mitochondrial motility in giant axonal neuropathy fibroblasts. Mol Biol Cell 2015; 27:608-16. [PMID: 26700320 PMCID: PMC4750921 DOI: 10.1091/mbc.e15-09-0627] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/18/2015] [Indexed: 11/17/2022] Open
Abstract
GAN patient cells have abnormal aggregates of vimentin intermediate filaments, to which mitochondria appear to be tethered. Motility of mitochondria, but not lysosomes, is inhibited in these cells. Transfection with wild-type gigaxonin (the protein mutated in this disease) disperses these aggregates and bundles, and mitochondrial motility returns to normal. Giant axonal neuropathy (GAN) is a rare disease caused by mutations in the GAN gene, which encodes gigaxonin, an E3 ligase adapter that targets intermediate filament (IF) proteins for degradation in numerous cell types, including neurons and fibroblasts. The cellular hallmark of GAN pathology is the formation of large aggregates and bundles of IFs. In this study, we show that both the distribution and motility of mitochondria are altered in GAN fibroblasts and this is attributable to their association with vimentin IF aggregates and bundles. Transient expression of wild-type gigaxonin in GAN fibroblasts reduces the number of IF aggregates and bundles, restoring mitochondrial motility. Conversely, silencing the expression of gigaxonin in control fibroblasts leads to changes in IF organization similar to that of GAN patient fibroblasts and a coincident loss of mitochondrial motility. The inhibition of mitochondrial motility in GAN fibroblasts is not due to a global inhibition of organelle translocation, as lysosome motility is normal. Our findings demonstrate that it is the pathological changes in IF organization that cause the loss of mitochondrial motility.
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Affiliation(s)
- Jason Lowery
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611
| | - Nikhil Jain
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611 Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Zurich 8093, Switzerland
| | - Edward R Kuczmarski
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611
| | - Saleemulla Mahammad
- Stem Cell and Cancer Research Institute, Michael DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Anne Goldman
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611
| | - Vladimir I Gelfand
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611
| | - Puneet Opal
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611
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40
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Ridge KM, Shumaker D, Robert A, Hookway C, Gelfand VI, Janmey PA, Lowery J, Guo M, Weitz DA, Kuczmarski E, Goldman RD. Methods for Determining the Cellular Functions of Vimentin Intermediate Filaments. Methods Enzymol 2015; 568:389-426. [PMID: 26795478 DOI: 10.1016/bs.mie.2015.09.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The type III intermediate filament protein vimentin was once thought to function mainly as a static structural protein in the cytoskeleton of cells of mesenchymal origin. Now, however, vimentin is known to form a dynamic, flexible network that plays an important role in a number of signaling pathways. Here, we describe various methods that have been developed to investigate the cellular functions of the vimentin protein and intermediate filament network, including chemical disruption, photoactivation and photoconversion, biolayer interferometry, soluble bead binding assay, three-dimensional substrate experiments, collagen gel contraction, optical-tweezer active microrheology, and force spectrum microscopy. Using these techniques, the contributions of vimentin to essential cellular processes can be probed in ever further detail.
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Affiliation(s)
- Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Chicago, Illinois, USA; Department of Cell and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA; Veterans Administration, Chicago, Illinois, USA.
| | - Dale Shumaker
- Division of Pulmonary and Critical Care Medicine, Chicago, Illinois, USA; Department of Cell and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Amélie Robert
- Department of Cell and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Caroline Hookway
- Department of Cell and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Vladimir I Gelfand
- Department of Cell and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Paul A Janmey
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Departments of Physiology and Physics & Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jason Lowery
- Division of Pulmonary and Critical Care Medicine, Chicago, Illinois, USA
| | - Ming Guo
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA; Department of Physics, Harvard University, Cambridge, Massachusetts, USA
| | - Edward Kuczmarski
- Department of Cell and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Robert D Goldman
- Division of Pulmonary and Critical Care Medicine, Chicago, Illinois, USA; Department of Cell and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
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41
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Bercht Pfleghaar K, Taimen P, Butin-Israeli V, Shimi T, Langer-Freitag S, Markaki Y, Goldman AE, Wehnert M, Goldman RD. Gene-rich chromosomal regions are preferentially localized in the lamin B deficient nuclear blebs of atypical progeria cells. Nucleus 2015; 6:66-76. [PMID: 25738644 DOI: 10.1080/19491034.2015.1004256] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
More than 20 mutations in the gene encoding A-type lamins (LMNA) cause progeria, a rare premature aging disorder. The major pathognomonic hallmarks of progeria cells are seen as nuclear deformations or blebs that are related to the redistribution of A- and B-type lamins within the nuclear lamina. However, the functional significance of these progeria-associated blebs remains unknown. We have carried out an analysis of the structural and functional consequences of progeria-associated nuclear blebs in dermal fibroblasts from a progeria patient carrying a rare point mutation p.S143F (C428T) in lamin A/C. These blebs form microdomains that are devoid of major structural components of the nuclear envelope (NE)/lamina including B-type lamins and nuclear pore complexes (NPCs) and are enriched in A-type lamins. Using laser capture microdissection and comparative genomic hybridization (CGH) analyses, we show that, while these domains are devoid of centromeric heterochromatin and gene-poor regions of chromosomes, they are enriched in gene-rich chromosomal regions. The active form of RNA polymerase II is also greatly enriched in blebs as well as nascent RNA but the nuclear co-activator SKIP is significantly reduced in blebs compared to other transcription factors. Our results suggest that the p.S143F progeria mutation has a severe impact not only on the structure of the lamina but also on the organization of interphase chromatin domains and transcription. These structural defects are likely to contribute to gene expression changes reported in progeria and other types of laminopathies.
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Affiliation(s)
- Katrin Bercht Pfleghaar
- a Department of Cell and Molecular Biology ; Feinberg School of Medicine; Northwestern University ; Chicago , IL USA
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42
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Dou Z, Xu C, Donahue G, Shimi T, Pan JA, Zhu J, Ivanov A, Capell BC, Drake AM, Shah PP, Catanzaro JM, Ricketts MD, Lamark T, Adam SA, Marmorstein R, Zong WX, Johansen T, Goldman RD, Adams PD, Berger SL. Autophagy mediates degradation of nuclear lamina. Nature 2015; 527:105-9. [PMID: 26524528 PMCID: PMC4824414 DOI: 10.1038/nature15548] [Citation(s) in RCA: 427] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/04/2015] [Indexed: 12/14/2022]
Abstract
Macroautophagy (hereafter referred to as autophagy) is a catabolic membrane trafficking process that degrades a variety of cellular constituents and is associated with human diseases. Although extensive studies have focused on autophagic turnover of cytoplasmic materials, little is known about the role of autophagy in degrading nuclear components. Here we report that the autophagy machinery mediates degradation of nuclear lamina components in mammals. The autophagy protein LC3/Atg8, which is involved in autophagy membrane trafficking and substrate delivery, is present in the nucleus and directly interacts with the nuclear lamina protein lamin B1, and binds to lamin-associated domains on chromatin. This LC3-lamin B1 interaction does not downregulate lamin B1 during starvation, but mediates its degradation upon oncogenic insults, such as by activated RAS. Lamin B1 degradation is achieved by nucleus-to-cytoplasm transport that delivers lamin B1 to the lysosome. Inhibiting autophagy or the LC3-lamin B1 interaction prevents activated RAS-induced lamin B1 loss and attenuates oncogene-induced senescence in primary human cells. Our study suggests that this new function of autophagy acts as a guarding mechanism protecting cells from tumorigenesis.
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Affiliation(s)
- Zhixun Dou
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Caiyue Xu
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Greg Donahue
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Takeshi Shimi
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ji-An Pan
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Jiajun Zhu
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrejs Ivanov
- Institute of Cancer Sciences, University of Glasgow, Cancer Research UK Beatson Labs, Glasgow G61 1BD, United Kingdom
| | - Brian C. Capell
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Adam M. Drake
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Parisha P. Shah
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Joseph M. Catanzaro
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794, USA
| | - M. Daniel Ricketts
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Trond Lamark
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø – The Arctic University of Norway, 9037 Tromsø, Norway
| | - Stephen A. Adam
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ronen Marmorstein
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Wei-Xing Zong
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Terje Johansen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø – The Arctic University of Norway, 9037 Tromsø, Norway
| | - Robert D. Goldman
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Peter D. Adams
- Institute of Cancer Sciences, University of Glasgow, Cancer Research UK Beatson Labs, Glasgow G61 1BD, United Kingdom
| | - Shelley L. Berger
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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43
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Abstract
The semiflexible polymers filamentous actin (F-actin) and intermediate filaments (IF) both form complex networks within the cell, and together are key determinants of cellular stiffness. While the mechanics of F-actin networks together with stiff microtubules have been characterized, the interplay between F-actin and IF networks is largely unknown, necessitating the study of composite networks using mixtures of semiflexible biopolymers. We employ bulk rheology in a simplified in vitro system to uncover the fundamental mechanical interactions between networks of the 2 semiflexible polymers, F-actin and vimentin IF. Surprisingly, co-polymerization of actin and vimentin can produce composite networks either stronger or weaker than pure F-actin networks. We show that this effect occurs through steric constraints imposed by IF on F-actin during network formation and filament crosslinking, highlighting novel emergent behavior in composite semiflexible networks.
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Affiliation(s)
- Mikkel H Jensen
- a School of Engineering and Applied Sciences ; Harvard University ; Cambridge , Massachusetts USA
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44
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Shimi T, Kittisopikul M, Tran J, Goldman AE, Adam SA, Zheng Y, Jaqaman K, Goldman RD. Structural organization of nuclear lamins A, C, B1, and B2 revealed by superresolution microscopy. Mol Biol Cell 2015; 26:4075-86. [PMID: 26310440 PMCID: PMC4710238 DOI: 10.1091/mbc.e15-07-0461] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/20/2015] [Indexed: 12/22/2022] Open
Abstract
Superresolution microscopy and computational image analysis demonstrate that the four nuclear lamin isoforms of mammalian cells are each organized into distinct meshwork structures sharing similar physical characteristics. Knockouts of single lamins alter the structure of the remaining lamins, suggesting interactions among the meshworks. The nuclear lamina is a key structural element of the metazoan nucleus. However, the structural organization of the major proteins composing the lamina is poorly defined. Using three-dimensional structured illumination microscopy and computational image analysis, we characterized the supramolecular structures of lamin A, C, B1, and B2 in mouse embryo fibroblast nuclei. Each isoform forms a distinct fiber meshwork, with comparable physical characteristics with respect to mesh edge length, mesh face area and shape, and edge connectivity to form faces. Some differences were found in face areas among isoforms due to variation in the edge lengths and number of edges per face, suggesting that each meshwork has somewhat unique assembly characteristics. In fibroblasts null for the expression of either lamins A/C or lamin B1, the remaining lamin meshworks are altered compared with the lamin meshworks in wild-type nuclei or nuclei lacking lamin B2. Nuclei lacking LA/C exhibit slightly enlarged meshwork faces and some shape changes, whereas LB1-deficient nuclei exhibit primarily a substantial increase in face area. These studies demonstrate that individual lamin isoforms assemble into complex networks within the nuclear lamina and that A- and B-type lamins have distinct roles in maintaining the organization of the nuclear lamina.
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Affiliation(s)
- Takeshi Shimi
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Mark Kittisopikul
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390
| | - Joseph Tran
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
| | - Anne E Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Yixian Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
| | - Khuloud Jaqaman
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
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Abstract
Intermediate filaments (IFs) are composed of one or more members of a large family of cytoskeletal proteins, whose expression is cell- and tissue type-specific. Their importance in regulating the physiological properties of cells is becoming widely recognized in functions ranging from cell motility to signal transduction. IF proteins assemble into nanoscale biopolymers with unique strain-hardening properties that are related to their roles in regulating the mechanical integrity of cells. Furthermore, mutations in the genes encoding IF proteins cause a wide range of human diseases. Due to the number of different types of IF proteins, we have limited this short review to cover structure and function topics mainly related to the simpler homopolymeric IF networks composed of vimentin, and specifically for diseases, the related muscle-specific desmin IF networks.
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Affiliation(s)
- Jason Lowery
- From the Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611 and
| | - Edward R Kuczmarski
- From the Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611 and
| | - Harald Herrmann
- the Division of Molecular Genetics (B060), German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Robert D Goldman
- From the Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611 and
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46
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Butin-Israeli V, Adam SA, Jain N, Otte GL, Neems D, Wiesmüller L, Berger SL, Goldman RD. Role of lamin b1 in chromatin instability. Mol Cell Biol 2015; 35:884-98. [PMID: 25535332 PMCID: PMC4323489 DOI: 10.1128/mcb.01145-14] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/01/2014] [Accepted: 12/18/2014] [Indexed: 01/14/2023] Open
Abstract
Nuclear lamins play important roles in the organization and structure of the nucleus; however, the specific mechanisms linking lamin structure to nuclear functions are poorly defined. We demonstrate that reducing nuclear lamin B1 expression by short hairpin RNA-mediated silencing in cancer cell lines to approximately 50% of normal levels causes a delay in the cell cycle and accumulation of cells in early S phase. The S phase delay appears to be due to the stalling and collapse of replication forks. The double-strand DNA breaks resulting from replication fork collapse were inefficiently repaired, causing persistent DNA damage signaling and the assembly of extensive repair foci on chromatin. The expression of multiple factors involved in DNA replication and repair by both nonhomologous end joining and homologous repair is misregulated when lamin B1 levels are reduced. We further demonstrate that lamin B1 interacts directly with the promoters of some genes associated with DNA damage response and repair, including BRCA1 and RAD51. Taken together, the results suggest that the maintenance of lamin B1 levels is required for DNA replication and repair through regulation of the expression of key factors involved in these essential nuclear functions.
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Affiliation(s)
- Veronika Butin-Israeli
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nikhil Jain
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Gabriel L Otte
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Daniel Neems
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm, Germany
| | - Shelly L Berger
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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47
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Chernoivanenko IS, Matveeva EA, Gelfand VI, Goldman RD, Minin AA. Mitochondrial membrane potential is regulated by vimentin intermediate filaments. FASEB J 2015; 29:820-7. [PMID: 25404709 PMCID: PMC4422353 DOI: 10.1096/fj.14-259903] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/06/2014] [Indexed: 11/11/2022]
Abstract
This study demonstrates that the association of mitochondria with vimentin intermediate filaments (VIFs) measurably increases their membrane potential. This increase is detected by quantitatively comparing the fluorescence intensity of mitochondria stained with the membrane potential-sensitive dye tetramethylrhodamine-ethyl ester (TMRE) in murine vimentin-null fibroblasts with that in the same cells expressing human vimentin (∼35% rise). When vimentin expression is silenced by small hairpin RNA (shRNA) to reduce vimentin by 90%, the fluorescence intensity of mitochondria decreases by 20%. The increase in membrane potential is caused by specific interactions between a subdomain of the non-α-helical N terminus (residues 40 to 93) of vimentin and mitochondria. In rho 0 cells lacking mitochondrial DNA (mtDNA) and consequently missing several key proteins in the mitochondrial respiratory chain (ρ(0) cells), the membrane potential generated by an alternative anaerobic process is insensitive to the interactions between mitochondria and VIF. The results of our studies show that the close association between mitochondria and VIF is important both for determining their position in cells and their physiologic activity.
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Affiliation(s)
- Ivan S Chernoivanenko
- *Institute of Protein Research, Russian Academy of Sciences, Group of Cell Biology, Moscow, Russia; and Department of Cell and Molecular Biology, Northwestern University's Feinberg School of Medicine, Chicago, Illinois, USA
| | - Elena A Matveeva
- *Institute of Protein Research, Russian Academy of Sciences, Group of Cell Biology, Moscow, Russia; and Department of Cell and Molecular Biology, Northwestern University's Feinberg School of Medicine, Chicago, Illinois, USA
| | - Vladimir I Gelfand
- *Institute of Protein Research, Russian Academy of Sciences, Group of Cell Biology, Moscow, Russia; and Department of Cell and Molecular Biology, Northwestern University's Feinberg School of Medicine, Chicago, Illinois, USA
| | - Robert D Goldman
- *Institute of Protein Research, Russian Academy of Sciences, Group of Cell Biology, Moscow, Russia; and Department of Cell and Molecular Biology, Northwestern University's Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alexander A Minin
- *Institute of Protein Research, Russian Academy of Sciences, Group of Cell Biology, Moscow, Russia; and Department of Cell and Molecular Biology, Northwestern University's Feinberg School of Medicine, Chicago, Illinois, USA
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48
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Jensen MH, Morris EJ, Goldman RD, Weitz DA. How Does the Interplay between Semiflexible Polymers Determine Composite Network Mechanics? Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.2474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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49
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Wood AM, Danielsen JMR, Lucas CA, Rice EL, Scalzo D, Shimi T, Goldman RD, Smith ED, Le Beau MM, Kosak ST. TRF2 and lamin A/C interact to facilitate the functional organization of chromosome ends. Nat Commun 2014; 5:5467. [PMID: 25399868 PMCID: PMC4235626 DOI: 10.1038/ncomms6467] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 10/03/2014] [Indexed: 12/28/2022] Open
Abstract
Telomeres protect the ends of linear genomes, and the gradual loss of telomeres is associated with cellular ageing. Telomere protection involves the insertion of the 3' overhang facilitated by telomere repeat-binding factor 2 (TRF2) into telomeric DNA, forming t-loops. We present evidence suggesting that t-loops can also form at interstitial telomeric sequences in a TRF2-dependent manner, forming an interstitial t-loop (ITL). We demonstrate that TRF2 association with interstitial telomeric sequences is stabilized by co-localization with A-type lamins (lamin A/C). We also find that lamin A/C interacts with TRF2 and that reduction in levels of lamin A/C or mutations in LMNA that cause an autosomal dominant premature ageing disorder--Hutchinson Gilford Progeria Syndrome (HGPS)-lead to reduced ITL formation and telomere loss. We propose that cellular and organismal ageing are intertwined through the effects of the interaction between TRF2 and lamin A/C on chromosome structure.
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Affiliation(s)
- Ashley M. Wood
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | | | - Catherine A. Lucas
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ellen L. Rice
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - David Scalzo
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Takeshi Shimi
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Robert D. Goldman
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Erica D. Smith
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Michelle M. Le Beau
- Section of Hematology/Oncology, Department of Medicine and Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois 60637, USA
| | - Steven T. Kosak
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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50
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Guo M, Ehrlicher AJ, Jensen MH, Renz M, Moore JR, Goldman RD, Lippincott-Schwartz J, Mackintosh FC, Weitz DA. Probing the stochastic, motor-driven properties of the cytoplasm using force spectrum microscopy. Cell 2014; 158:822-832. [PMID: 25126787 PMCID: PMC4183065 DOI: 10.1016/j.cell.2014.06.051] [Citation(s) in RCA: 323] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/28/2014] [Accepted: 06/29/2014] [Indexed: 01/17/2023]
Abstract
Molecular motors in cells typically produce highly directed motion; however, the aggregate, incoherent effect of all active processes also creates randomly fluctuating forces, which drive diffusive-like, nonthermal motion. Here, we introduce force-spectrum-microscopy (FSM) to directly quantify random forces within the cytoplasm of cells and thereby probe stochastic motor activity. This technique combines measurements of the random motion of probe particles with independent micromechanical measurements of the cytoplasm to quantify the spectrum of force fluctuations. Using FSM, we show that force fluctuations substantially enhance intracellular movement of small and large components. The fluctuations are three times larger in malignant cells than in their benign counterparts. We further demonstrate that vimentin acts globally to anchor organelles against randomly fluctuating forces in the cytoplasm, with no effect on their magnitude. Thus, FSM has broad applications for understanding the cytoplasm and its intracellular processes in relation to cell physiology in healthy and diseased states.
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Affiliation(s)
- Ming Guo
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Allen J Ehrlicher
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Mikkel H Jensen
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Physiology and Biophysics, Boston University, Boston, MA 02118, USA
| | - Malte Renz
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey R Moore
- Department of Physiology and Biophysics, Boston University, Boston, MA 02118, USA
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jennifer Lippincott-Schwartz
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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