1
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Wang N, Floriano Marcelino T, Ade C, Pendlmayr S, Ramos Docampo MA, Städler B. Collagenase motors in gelatine-based hydrogels. Nanoscale 2024. [PMID: 38690802 DOI: 10.1039/d3nr05712g] [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] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Nano/micromotors outperform Brownian motion due to their self-propulsive capabilities and hold promise as carriers for drug delivery across biological barriers such as the extracellular matrix. This study employs poly(2-(diethylamino)ethyl methacrylate) polymer brushes to enhance the collagenase-loading capacity of silica particle-based motors with the aim to systematically investigate the impact of gelatine viscosity, motors' size, and morphology on their propulsion velocity. Notably, 500 nm and 1 μm motors achieve similar speeds as high as ∼15 μm s-1 in stiff gelatine-based hydrogels when triggered with calcium. Taken together, our findings highlight the potential of collagenase-based motors for navigating the extracellular matrix, positioning them as promising candidates for efficient drug delivery.
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Affiliation(s)
- Nanying Wang
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark.
| | - Thaís Floriano Marcelino
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark.
- Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Carina Ade
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark.
| | - Stefan Pendlmayr
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark.
- Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Miguel A Ramos Docampo
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark.
| | - Brigitte Städler
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark.
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2
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Zhao L, Arias SL, Zipfel W, Brito IL, Yeo J. Coarse-grained modeling and dynamics tracking of nanoparticles diffusion in human gut mucus. Int J Biol Macromol 2024; 267:131434. [PMID: 38614182 DOI: 10.1016/j.ijbiomac.2024.131434] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/23/2024] [Accepted: 04/04/2024] [Indexed: 04/15/2024]
Abstract
The gastrointestinal (GI) tract's mucus layer serves as a critical barrier and a mediator in drug nanoparticle delivery. The mucus layer's diverse molecular structures and spatial complexity complicates the mechanistic study of the diffusion dynamics of particulate materials. In response, we developed a bi-component coarse-grained mucus model, specifically tailored for the colorectal cancer environment, that contained the two most abundant glycoproteins in GI mucus: Muc2 and Muc5AC. This model demonstrated the effects of molecular composition and concentration on mucus pore size, a key determinant in the permeability of nanoparticles. Using this computational model, we investigated the diffusion rate of polyethylene glycol (PEG) coated nanoparticles, a widely used muco-penetrating nanoparticle. We validated our model with experimentally characterized mucus pore sizes and the diffusional coefficients of PEG-coated nanoparticles in the mucus collected from cultured human colorectal goblet cells. Machine learning fingerprints were then employed to provide a mechanistic understanding of nanoparticle diffusional behavior. We found that larger nanoparticles tended to be trapped in mucus over longer durations but exhibited more ballistic diffusion over shorter time spans. Through these discoveries, our model provides a promising platform to study pharmacokinetics in the GI mucus layer.
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Affiliation(s)
- Liming Zhao
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
| | - Sandra L Arias
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Warren Zipfel
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA.
| | - Jingjie Yeo
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA.
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3
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Perez AJ, Lamanna MM, Bruce KE, Touraev MA, Page JE, Shaw SL, Tsui HCT, Winkler ME. Elongasome core proteins and class A PBP1a display zonal, processive movement at the midcell of Streptococcus pneumoniae. bioRxiv 2024:2024.01.10.575112. [PMID: 38328058 PMCID: PMC10849506 DOI: 10.1101/2024.01.10.575112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Ovoid-shaped bacteria, such as Streptococcus pneumoniae (pneumococcus), have two spatially separated peptidoglycan (PG) synthase nanomachines that locate zonally to the midcell of dividing cells. The septal PG synthase bPBP2x:FtsW closes the septum of dividing pneumococcal cells, whereas the elongasome located on the outer edge of the septal annulus synthesizes peripheral PG outward. We showed previously by sm-TIRFm that the septal PG synthase moves circumferentially at midcell, driven by PG synthesis and not by FtsZ treadmilling. The pneumococcal elongasome consists of the PG synthase bPBP2b:RodA, regulators MreC, MreD, and RodZ, but not MreB, and genetically associated proteins Class A aPBP1a and muramidase MpgA. Given its zonal location separate from FtsZ, it was of considerable interest to determine the dynamics of proteins in the pneumococcal elongasome. We found that bPBP2b, RodA, and MreC move circumferentially with the same velocities and durations at midcell, driven by PG synthesis. However, outside of the midcell zone, the majority of these elongasome proteins move diffusively over the entire surface of cells. Depletion of MreC resulted in loss of circumferential movement of bPBP2b, and bPBP2b and RodA require each other for localization and circumferential movement. Notably, a fraction of aPBP1a molecules also moved circumferentially at midcell with velocities similar to those of components of the core elongasome, but for shorter durations. Other aPBP1a molecules were static at midcell or diffusing over cell bodies. Last, MpgA displayed non-processive, subdiffusive motion that was largely confined to the midcell region and less frequently detected over the cell body.
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4
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Richard CA, Seum C, Gonzalez-Gaitan M. Microtubule polarity determines the lineage of embryonic neural precursor in zebrafish spinal cord. Commun Biol 2024; 7:439. [PMID: 38600297 PMCID: PMC11006876 DOI: 10.1038/s42003-024-06018-7] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/06/2024] [Indexed: 04/12/2024] Open
Abstract
The phenomenal diversity of neuronal types in the central nervous system is achieved in part by the asymmetric division of neural precursors. In zebrafish neural precursors, asymmetric dispatch of Sara endosomes (with its Notch signaling cargo) functions as fate determinant which mediates asymmetric division. Here, we found two distinct pools of neural precursors based on Sara endosome inheritance and spindle-microtubule enrichment. Symmetric or asymmetric levels of spindle-microtubules drive differently Sara endosomes inheritance and predict neural precursor lineage. We uncover that CAMSAP2a/CAMSAP3a and KIF16Ba govern microtubule asymmetry and endosome motility, unveiling the heterogeneity of neural precursors. Using a plethora of physical and cell biological assays, we determined the physical parameters and molecular mechanisms behind microtubule asymmetries and biased endosome motility. Evolutionarily, the values of those parameters explain why all sensory organ precursor cells are asymmetric in flies while, in zebrafish spinal cord, two populations of neural precursors (symmetric vs asymmetric) are possible.
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Affiliation(s)
- Clément-Alexis Richard
- Department of Biochemistry, Faculty of Science, University of Geneva, 30 Quai Ernest Ansermet, Geneva, 1205, Switzerland.
| | - Carole Seum
- Department of Biochemistry, Faculty of Science, University of Geneva, 30 Quai Ernest Ansermet, Geneva, 1205, Switzerland
| | - Marcos Gonzalez-Gaitan
- Department of Biochemistry, Faculty of Science, University of Geneva, 30 Quai Ernest Ansermet, Geneva, 1205, Switzerland.
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5
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Nikalayevich E, Letort G, de Labbey G, Todisco E, Shihabi A, Turlier H, Voituriez R, Yahiatene M, Pollet-Villard X, Innocenti M, Schuh M, Terret ME, Verlhac MH. Aberrant cortex contractions impact mammalian oocyte quality. Dev Cell 2024; 59:841-852.e7. [PMID: 38387459 DOI: 10.1016/j.devcel.2024.01.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/18/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
The cortex controls cell shape. In mouse oocytes, the cortex thickens in an Arp2/3-complex-dependent manner, ensuring chromosome positioning and segregation. Surprisingly, we identify that mouse oocytes lacking the Arp2/3 complex undergo cortical actin remodeling upon division, followed by cortical contractions that are unprecedented in mammalian oocytes. Using genetics, imaging, and machine learning, we show that these contractions stir the cytoplasm, resulting in impaired organelle organization and activity. Oocyte capacity to avoid polyspermy is impacted, leading to a reduced female fertility. We could diminish contractions and rescue cytoplasmic anomalies. Similar contractions were observed in human oocytes collected as byproducts during IVF (in vitro fertilization) procedures. These contractions correlate with increased cytoplasmic motion, but not with defects in spindle assembly or aneuploidy in mice or humans. Our study highlights a multiscale effect connecting cortical F-actin, contractions, and cytoplasmic organization and affecting oocyte quality, with implications for female fertility.
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Affiliation(s)
- Elvira Nikalayevich
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, Université PSL, CNRS, INSERM, 75005 Paris, France
| | - Gaëlle Letort
- Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, Université Paris Cité, 25 rue du Dr. Roux, 75015 Paris, France
| | - Ghislain de Labbey
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, Université PSL, CNRS, INSERM, 75005 Paris, France
| | - Elena Todisco
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Anastasia Shihabi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, Université PSL, CNRS, INSERM, 75005 Paris, France
| | - Hervé Turlier
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, Université PSL, CNRS, INSERM, 75005 Paris, France
| | - Raphaël Voituriez
- Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Laboratoire Jean Perrin, CNRS, Sorbonne Université, Paris, France
| | - Mohamed Yahiatene
- Centre Assistance Médicale à la Procréation Nataliance, Groupe Mlab, Pôle Santé Oréliance, Saran, France
| | - Xavier Pollet-Villard
- Centre Assistance Médicale à la Procréation Nataliance, Groupe Mlab, Pôle Santé Oréliance, Saran, France
| | - Metello Innocenti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Melina Schuh
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Marie-Emilie Terret
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, Université PSL, CNRS, INSERM, 75005 Paris, France.
| | - Marie-Hélène Verlhac
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, Université PSL, CNRS, INSERM, 75005 Paris, France.
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6
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Ye Y, Homer HA. A surge in cytoplasmic viscosity triggers nuclear remodeling required for Dux silencing and pre-implantation embryo development. Cell Rep 2024; 43:113917. [PMID: 38446665 DOI: 10.1016/j.celrep.2024.113917] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/17/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Embryonic genome activation (EGA) marks the transition from dependence on maternal transcripts to an embryonic transcriptional program. The precise temporal regulation of gene expression, specifically the silencing of the Dux/murine endogenous retrovirus type L (MERVL) program during late 2-cell interphase, is crucial for developmental progression in mouse embryos. How this finely tuned regulation is achieved within this specific window is poorly understood. Here, using particle-tracking microrheology throughout the mouse oocyte-to-embryo transition, we identify a surge in cytoplasmic viscosity specific to late 2-cell interphase brought about by high microtubule and endomembrane density. Importantly, preventing the rise in 2-cell viscosity severely impairs nuclear reorganization, resulting in a persistently open chromatin configuration and failure to silence Dux/MERVL. This, in turn, derails embryo development beyond the 2- and 4-cell stages. Our findings reveal a mechanical role of the cytoplasm in regulating Dux/MERVL repression via nuclear remodeling during a temporally confined period in late 2-cell interphase.
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Affiliation(s)
- Yunan Ye
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia
| | - Hayden Anthony Homer
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia.
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7
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Kim JM, Carcamo CC, Jazani S, Xie Z, Feng XA, Yamadi M, Poyton M, Holland KL, Grimm JB, Lavis LD, Ha T, Wu C. Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers. eLife 2024; 12:RP91433. [PMID: 38497611 PMCID: PMC10948146 DOI: 10.7554/elife.91433] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024] Open
Abstract
Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement, and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and two-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding, respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/s on extended linear DNA under tension. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.
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Affiliation(s)
- Jee Min Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Claudia C Carcamo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Sina Jazani
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Zepei Xie
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Xinyu A Feng
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Maryam Yamadi
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Matthew Poyton
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Katie L Holland
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
- Howard Hughes Medical InstituteBostonUnited States
| | - Carl Wu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Molecular Biology and Genetics, Johns Hopkins School of MedicineBaltimoreUnited States
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8
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Cai G, Li X, Lin SS, Chen SJ, Rodgers NC, Koning KM, Bi D, Liu AP. Matrix confinement modulates 3D spheroid sorting and burst-like collective migration. Acta Biomater 2024:S1742-7061(24)00126-0. [PMID: 38490482 DOI: 10.1016/j.actbio.2024.03.007] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/17/2024]
Abstract
While it is known that cells with differential adhesion tend to segregate and preferentially sort, the physical forces governing sorting and invasion in heterogeneous tumors remain poorly understood. To investigate this, we tune matrix confinement, mimicking changes in the stiffness and confinement of the tumor microenvironment, to explore how physical confinement influences individual and collective cell migration in 3D spheroids. High levels of confinement lead to cell sorting while reducing matrix confinement triggers the collective fluidization of cell motion. Cell sorting, which depends on cell-cell adhesion, is crucial to this phenomenon. Burst-like migration does not occur for spheroids that have not undergone sorting, regardless of the degree of matrix confinement. Using computational Self-Propelled Voronoi modeling, we show that spheroid sorting and invasion into the matrix depend on the balance between cell-generated forces and matrix resistance. The findings support a model where matrix confinement modulates 3D spheroid sorting and unjamming in an adhesion-dependent manner, providing insights into the mechanisms of cell sorting and migration in the primary tumor and toward distant metastatic sites. STATEMENT OF SIGNIFICANCE: The mechanical properties of the tumor microenvironment significantly influence cancer cell migration within the primary tumor, yet how these properties affect intercellular interactions in heterogeneous tumors is not well understood. By utilizing calcium and calcium chelators, we dynamically alter collagen-alginate hydrogel stiffness and investigate tumor cell behavior within co-culture spheroids in response to varying degrees of matrix confinement. High confinement is found to trigger cell sorting while reducing confinement for sorted spheroids facilitates collective cell invasion. Notably, without prior sorting, spheroids do not exhibit burst-like migration, regardless of confinement levels. This work establishes that matrix confinement and intercellular adhesion regulate 3D spheroid dynamics, offering insights into cellular organization and migration within the primary tumor.
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Affiliation(s)
- Grace Cai
- Applied Physics Program, University of Michigan, Ann Arbor, MI, USA
| | - Xinzhi Li
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Shan-Shan Lin
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Samuel J Chen
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Nicole C Rodgers
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Katherine M Koning
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Dapeng Bi
- Department of Physics, Northeastern University, Boston, MA, USA.
| | - Allen P Liu
- Applied Physics Program, University of Michigan, Ann Arbor, MI, USA; Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA; Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
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9
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Dukhno O, Ghosh S, Greiner V, Bou S, Godet J, Muhr V, Buchner M, Hirsch T, Mély Y, Przybilla F. Targeted Single Particle Tracking with Upconverting Nanoparticles. ACS Appl Mater Interfaces 2024; 16:11217-11227. [PMID: 38386424 DOI: 10.1021/acsami.3c17116] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Single particle tracking (SPT) is a powerful technique for real-time microscopic visualization of the movement of individual biomolecules within or on the surface of living cells. However, SPT often suffers from the suboptimal performance of the photon-emitting labels used to tag the biomolecules of interest. For example, fluorescent dyes have poor photostability, while quantum dots suffer from blinking that hampers track acquisition and interpretation. Upconverting nanoparticles (UCNPs) have recently emerged as a promising anti-Stokes luminescent label for SPT. In this work, we demonstrated targeted SPT using UCNPs. For this, we synthesized 30 nm diameter doped UCNPs and coated them with amphiphilic polymers decorated with polyethylene glycol chains to make them water-dispersible and minimize their nonspecific interactions with cells. Coated UCNPs highly homogeneous in brightness (as confirmed by a single particle investigation) were functionalized by immunoglobulin E (IgE) using a biotin-streptavidin strategy. Using these IgE-UCNP SPT labels, we tracked high-affinity IgE receptors (FcεRI) on the membrane of living RBL-2H3 mast cells at 37 °C in the presence and absence of antigen and obtained good agreement with the literature. Moreover, we used the FcεRI-IgE receptor-antibody system to directly compare the performance of UCNP-based SPT labels to organic dyes (AlexaFluor647) and quantum dots (QD655). Due to their photostability as well as their backgroundless and continuous luminescence, SPT trajectories obtained with UCNP labels are no longer limited by the photophysics of the label but only by the dynamics of the system and, in particular, the movement of the label out of the field of view and/or focal plane.
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Affiliation(s)
- Oleksii Dukhno
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Srijayee Ghosh
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Vanille Greiner
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Sophie Bou
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Julien Godet
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
- IMAGeS team at ICube, UMR 7357, CNRS, Université de Strasbourg, Strasbourg 67000, France
| | - Verena Muhr
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
| | - Markus Buchner
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
| | - Thomas Hirsch
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
| | - Yves Mély
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Frédéric Przybilla
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
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10
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Cai G, Li X, Lin SS, Chen SJ, Rodgers NC, Koning KM, Bi D, Liu AP. Matrix confinement modulates 3D spheroid sorting and burst-like collective migration. bioRxiv 2024:2023.07.23.549940. [PMID: 37546827 PMCID: PMC10401934 DOI: 10.1101/2023.07.23.549940] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
While it is known that cells with differential adhesion tend to segregate and preferentially sort, the physical forces governing sorting and invasion in heterogeneous tumors remain poorly understood. To investigate this, we tune matrix confinement, mimicking changes in the stiffness and confinement of the tumor microenvironment, to explore how physical confinement influences individual and collective cell migration in 3D spheroids. High levels of confinement lead to cell sorting while reducing matrix confinement triggers the collective fluidization of cell motion. Cell sorting, which depends on cell-cell adhesion, is crucial to this phenomenon. Burst-like migration does not occur for spheroids that have not undergone sorting, regardless of the degree of matrix confinement. Using computational Self-Propelled Voronoi modeling, we show that spheroid sorting and invasion into the matrix depend on the balance between cell-generated forces and matrix resistance. The findings support a model where matrix confinement modulates 3D spheroid sorting and unjamming in an adhesion-dependent manner, providing insights into the mechanisms of cell sorting and migration in the primary tumor and toward distant metastatic sites.
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Affiliation(s)
- Grace Cai
- Applied Physics Program, University of Michigan, Ann Arbor, MI, USA
| | - Xinzhi Li
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Shan-Shan Lin
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Samuel J. Chen
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Nicole C. Rodgers
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Katherine M. Koning
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Dapeng Bi
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Allen P. Liu
- Applied Physics Program, University of Michigan, Ann Arbor, MI, USA
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
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11
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Wu K, Wang B, Cao B, Ma W, Zhang Y, Cheng Y, Hu J, Gao Y. Protective role of pyrroloquinoline quinone against gentamicin induced cochlear hair cell ototoxicity. J Appl Toxicol 2024; 44:235-244. [PMID: 37650462 DOI: 10.1002/jat.4535] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023]
Abstract
Gentamicin (GM) is one of the commonly used antibiotics in the aminoglycoside class but is ototoxic, which constantly impacts the quality of human life. Pyrroloquinoline quinone (PQQ) as a redox cofactor produced by bacteria was found in soil and foods that exert an antioxidant and redox modulator. It is well documented that the PQQ can alleviate inflammatory responses and cytotoxicity. However, our understanding of PQQ in ototoxicity remains unclear. We reported that PQQ could protect against GM-induced ototoxicity in House Ear Institute-Organ of Corti 1 (HEI-OC1) cells in vitro. To evaluate reactive oxygen species (ROS) production and mitochondrial function, ROS and JC-1 staining, oxygen consumption rate (OCR), and extracellular acidification rate (ECAR) measurements in living cells, mitochondrial dynamics analysis was performed. GM-mediated damage was performed by reducing the production of ROS and inhibiting mitochondria biogenesis and dynamics. PQQ ameliorated the cellular oxidative stress and recovered mitochondrial membrane potential, facilitating the recovery of mitochondrial biogenesis and dynamics. Our in vitro findings improve our understanding of the GM-induced ototoxicity with therapeutic implications for PQQ.
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Affiliation(s)
- Kunyi Wu
- Core Research Laboratory, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Botao Wang
- Department of Otolaryngology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Bo Cao
- Core Research Laboratory, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Weijun Ma
- Department of Otolaryngology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yan Zhang
- Department of Otolaryngology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ying Cheng
- Department of Otolaryngology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Juan Hu
- Department of Otolaryngology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ying Gao
- Department of Otolaryngology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
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12
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Ramos Docampo MA, Hovorka O, Städler B. Magnetic micromotors crossing lipid membranes. Nanoscale 2024; 16:2432-2443. [PMID: 38226699 DOI: 10.1039/d3nr05462d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Nano/micromotors are self-propelled particles that show enhanced motion upon being triggered by a stimulus. Their use in nanomedicine has been widely explored, with special focus on imaging or drug delivery. However, a thorough understanding of the requirements for more efficient locomotion is still lacking. In this paper, we assembled magnetically propelled motors of different sizes (i.e., 0.5, 1 and 4 μm) and surface chemistries (positive charge or PEGylated) and assessed their motion in the presence of giant unilamellar lipid vesicles (GUVs) of varying compositions (zwitterionic, negatively charged and saturated lipids). Unexpectedly, the size does not seem to be the dominating characteristics that governs the ability of the motors to cross lipid membranes. Specifically, the 0.5 μm PEGylated motors have very limited ability to cross the lipid membrane of GUVs due to their non-interacting nature compared to their equally sized positively charged counterparts. Furthermore, membranes made of saturated lipids and, in particular, in combination with a weak magnetic field facilitate motors' crossing, regardless of their size. The results were validated by in-house data-driven statistical analysis that employs experimental data to allow for the identification of individual motor motion in the ensemble when meeting the lipid membranes. Altogether, we provide insight into motor locomotion when they interact with a biological barrier considering both the entire ensemble and the individual motors, which has the potential to support considerations of future motor designs.
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Affiliation(s)
- Miguel A Ramos Docampo
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark.
| | - Ondrej Hovorka
- Faculty of Engineering and Physical Sciences, University of Southampton, SO16 7QF, Southampton, UK
| | - Brigitte Städler
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark.
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13
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Zhang Z, Rong X, Xie T, Li Z, Song H, Zhen S, Wang H, Wu J, Jaffrey SR, Li X. Fluorogenic CRISPR for genomic DNA imaging. Nat Commun 2024; 15:934. [PMID: 38296979 PMCID: PMC10831063 DOI: 10.1038/s41467-024-45163-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
Genomic DNA exhibits high heterogeneity in terms of its dynamic within the nucleus, its structure and functional roles. CRISPR-based imaging approaches can image genomic loci in living cells. However, conventional CRISPR-based tools involve expressing constitutively fluorescent proteins, resulting in high background and nonspecific nucleolar signal. Here, we construct fluorogenic CRISPR (fCRISPR) to overcome these issues. fCRISPR is designed with dCas9, an engineered sgRNA, and a fluorogenic protein. Fluorogenic proteins are degraded unless they are bound to specific RNA hairpins. These hairpins are inserted into sgRNA, resulting in dCas9: sgRNA: fluorogenic protein ternary complexes that enable fluorogenic DNA imaging. With fCRISPR, we image various genomic DNA in different human cells with high signal-to-noise ratio and sensitivity. Furthermore, fCRISPR tracks chromosomes dynamics and length. fCRISPR also allows DNA double-strand breaks (DSBs) and repair to be tracked in real time. Taken together, fCRISPR offers a high-contrast and sensitive platform for imaging genomic loci.
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Affiliation(s)
- Zhongxuan Zhang
- Beijing Institute of Life Sciences, Chinese Academy of Science, 100101, Beijing, China
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, 646000, Luzhou, Sichuan, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiaoxiao Rong
- Beijing Institute of Life Sciences, Chinese Academy of Science, 100101, Beijing, China
- College of Life Science, Hebei University, Baoding, 071002, Hebei, China
| | - Tianjin Xie
- Beijing Institute of Life Sciences, Chinese Academy of Science, 100101, Beijing, China
- School of Chemistry and Chemical Engineering, Southwest University, Beibei District, 400715, Chongqing, China
| | - Zehao Li
- Beijing Institute of Life Sciences, Chinese Academy of Science, 100101, Beijing, China
- College of Life Science, Hebei University, Baoding, 071002, Hebei, China
| | - Haozhi Song
- Beijing Institute of Life Sciences, Chinese Academy of Science, 100101, Beijing, China
| | - Shujun Zhen
- School of Chemistry and Chemical Engineering, Southwest University, Beibei District, 400715, Chongqing, China
| | - Haifeng Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China
| | - Jiahui Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | - Xing Li
- Beijing Institute of Life Sciences, Chinese Academy of Science, 100101, Beijing, China.
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, 646000, Luzhou, Sichuan, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
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14
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Heinrich S, Hondele M, Marchand D, Derrer CP, Zedan M, Oswald A, Malinovska L, Uliana F, Khawaja S, Mancini R, Grunwald D, Weis K. Glucose stress causes mRNA retention in nuclear Nab2 condensates. Cell Rep 2024; 43:113593. [PMID: 38113140 DOI: 10.1016/j.celrep.2023.113593] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 10/12/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023] Open
Abstract
Nuclear mRNA export via nuclear pore complexes is an essential step in eukaryotic gene expression. Although factors involved in mRNA transport have been characterized, a comprehensive mechanistic understanding of this process and its regulation is lacking. Here, we use single-RNA imaging in yeast to show that cells use mRNA retention to control mRNA export during stress. We demonstrate that, upon glucose withdrawal, the essential RNA-binding factor Nab2 forms RNA-dependent condensate-like structures in the nucleus. This coincides with a reduced abundance of the DEAD-box ATPase Dbp5 at the nuclear pore. Depleting Dbp5, and consequently blocking mRNA export, is necessary and sufficient to trigger Nab2 condensation. The state of Nab2 condensation influences the extent of nuclear mRNA accumulation and can be recapitulated in vitro, where Nab2 forms RNA-dependent liquid droplets. We hypothesize that cells use condensation to regulate mRNA export and control gene expression during stress.
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Affiliation(s)
- Stephanie Heinrich
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland.
| | - Maria Hondele
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland; Biozentrum, Center for Molecular Life Sciences, University of Basel, 4056 Basel, Switzerland
| | - Désirée Marchand
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Carina Patrizia Derrer
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Mostafa Zedan
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Alexandra Oswald
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Liliana Malinovska
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Federico Uliana
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Sarah Khawaja
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - Roberta Mancini
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland
| | - David Grunwald
- University of Massachusetts Chan Medical School, RNA Therapeutics Institute, Worcester, MA 01605, USA
| | - Karsten Weis
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), 8093 Zurich, Switzerland.
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15
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Kim JM, Carcamo CC, Jazani S, Xie Z, Feng XA, Yamadi M, Poyton M, Holland KL, Grimm JB, Lavis LD, Ha T, Wu C. Dynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin Remodelers. bioRxiv 2024:2023.06.13.544671. [PMID: 38293098 PMCID: PMC10827135 DOI: 10.1101/2023.06.13.544671] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start-sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and 2-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/sec on extended linear DNA under tension. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.
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Affiliation(s)
- Jee Min Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Claudia C. Carcamo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sina Jazani
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zepei Xie
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xinyu A. Feng
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Maryam Yamadi
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Poyton
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Katie L. Holland
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
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16
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Yu W, Tingey M, Kelich JM, Li Y, Yu J, Junod SL, Jiang Z, Hansen I, Good N, Yang W. Exploring Cellular Gateways: Unraveling the Secrets of Disordered Proteins within Live Nuclear Pores. Res Sq 2024:rs.3.rs-3504130. [PMID: 38260360 PMCID: PMC10802689 DOI: 10.21203/rs.3.rs-3504130/v1] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Understanding the spatial organization of nucleoporins (Nups) with intrinsically disordered domains within the nuclear pore complex (NPC) is crucial for deciphering eukaryotic nucleocytoplasmic transport. Leveraging high-speed 2D single-molecule tracking and virtual 3D super-resolution microscopy in live HeLa cells, we investigated the spatial distribution of all eleven phenylalanine-glycine (FG)-rich Nups within individual NPCs. Our study reveals a nuanced landscape of FG-Nup conformations and arrangements. Five FG-Nups are steadfastly anchored at the NPC scaffold, collectively shaping a central doughnut-shaped channel, while six others exhibit heightened flexibility, extending towards the cytoplasmic and nucleoplasmic regions. Intriguingly, Nup214 and Nup153 contribute to cap-like structures that dynamically alternate between open and closed states along the nucleocytoplasmic transport axis, impacting the cytoplasmic and nuclear sides, respectively. Furthermore, Nup98, concentrated at the scaffold region, extends throughout the entire NPC while overlapping with other FG-Nups. Together, these eleven FG-Nups compose a versatile, capped trichoid channel spanning approximately 270 nm across the nuclear envelope. This adaptable trichoid channel facilitates a spectrum of pathways for passive diffusion and facilitated nucleocytoplasmic transport. Our comprehensive mapping of FG-Nup organization within live NPCs offers a unifying mechanism accommodating multiple transport pathways, thereby advancing our understanding of cellular transport processes.
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Affiliation(s)
- Wenlan Yu
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Mark Tingey
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Joseph M. Kelich
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Yichen Li
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Jingjie Yu
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Samuel L. Junod
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Zecheng Jiang
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Ian Hansen
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Nacef Good
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
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17
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Xie H, Han X, Xiao G, Xu H, Zhang Y, Zhang G, Li Q, He J, Zhu D, Yu X, Dai Q. Multifocal fluorescence video-rate imaging of centimetre-wide arbitrarily shaped brain surfaces at micrometric resolution. Nat Biomed Eng 2023:10.1038/s41551-023-01155-6. [PMID: 38057428 DOI: 10.1038/s41551-023-01155-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/26/2023] [Indexed: 12/08/2023]
Abstract
Fluorescence microscopy allows for the high-throughput imaging of cellular activity across brain areas in mammals. However, capturing rapid cellular dynamics across the curved cortical surface is challenging, owing to trade-offs in image resolution, speed, field of view and depth of field. Here we report a technique for wide-field fluorescence imaging that leverages selective illumination and the integration of focal areas at different depths via a spinning disc with varying thickness to enable video-rate imaging of previously reconstructed centimetre-scale arbitrarily shaped surfaces at micrometre-scale resolution and at a depth of field of millimetres. By implementing the technique in a microscope capable of acquiring images at 1.68 billion pixels per second and resolving 16.8 billion voxels per second, we recorded neural activities and the trajectories of neutrophils in real time on curved cortical surfaces in live mice. The technique can be integrated into many microscopes and macroscopes, in both reflective and fluorescence modes, for the study of multiscale cellular interactions on arbitrarily shaped surfaces.
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Affiliation(s)
- Hao Xie
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
| | - Xiaofei Han
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Guihua Xiao
- Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China
| | - Hanyun Xu
- Department of Neurosurgery, The First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yuanlong Zhang
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Guoxun Zhang
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Qingwei Li
- School of Medicine, Tsinghua University, Beijing, China
| | - Jing He
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, China
| | - Xinguang Yu
- Department of Neurosurgery, The First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
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18
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Hatakeyama H, Oshima T, Ono S, Morimoto Y, Takahashi N. Single-molecule analysis of intracellular insulin granule behavior and its application to analyzing cytoskeletal dependence and pathophysiological implications. Front Physiol 2023; 14:1287275. [PMID: 38124716 PMCID: PMC10731264 DOI: 10.3389/fphys.2023.1287275] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction: Mobilization of intracellular insulin granules to the plasma membrane plays a crucial role in regulating insulin secretion. However, the regulatory mechanisms of this mobilization process have been poorly understood due to technical limitations. In this study, we propose a convenient approach for assessing intracellular insulin granule behavior based on single-molecule analysis of insulin granule membrane proteins labeled with Quantum dot fluorescent nanocrystals. Methods: This approach allows us to analyze intracellular insulin granule movement with subpixel accuracy at 33 fps. We tracked two insulin granule membrane proteins, phogrin and zinc transporter 8, fused to HaloTag in rat insulinoma INS-1 cells and, by evaluating the tracks with mean-square displacement, demonstrated the characteristic behavior of insulin granules. Results and discussion: Pharmacological perturbations of microtubules and F-actin affected insulin granule behavior on distinct modalities. Specifically, microtubule dynamics and F-actin positively and negatively regulate insulin granule behavior, respectively, presumably by modulating each different behavioral mode. Furthermore, we observed impaired insulin granule behavior and cytoskeletal architecture under chronic treatment of high concentrations of glucose and palmitate. Our approach provides detailed information regarding intracellular insulin granule mobilization and its pathophysiological implications. This study sheds new light on the regulatory mechanisms of intracellular insulin granule mobilization and has important implications for understanding the pathogenesis of diabetes.
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Affiliation(s)
- Hiroyasu Hatakeyama
- Department of Physiology, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Tomomi Oshima
- Department of Physiology, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Shinichiro Ono
- Department of Physiology, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Yuichi Morimoto
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institute for Advanced Study (UTIAS), The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory of Structural Physiology, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Noriko Takahashi
- Department of Physiology, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
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19
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Wells MJ, Currie H, Gordon VD. Physiological Concentrations of Calcium Interact with Alginate and Extracellular DNA in the Matrices of Pseudomonas aeruginosa Biofilms to Impede Phagocytosis by Neutrophils. Langmuir 2023; 39:17050-17058. [PMID: 37972353 PMCID: PMC10764079 DOI: 10.1021/acs.langmuir.3c01637] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Biofilms are communities of interacting microbes embedded in a matrix of polymer, protein, and other materials. Biofilms develop distinct mechanical characteristics that depend on their predominant matrix components. These matrix components may be produced by microbes themselves or, for infections in vivo, incorporated from the host environment. Pseudomonas aeruginosa (P. aeruginosa) is a human pathogen that forms robust biofilms that extensively tolerate antibiotics and effectively evade clearance by the immune system. Two of the important bacterial-produced polymers in the matrices of P. aeruginosa biofilms are alginate and extracellular DNA (eDNA), both of which are anionic and therefore have the potential to interact electrostatically with cations. Many physiological sites of infection contain significant concentrations of the calcium ion (Ca2+). In this study, we investigate the structural and mechanical impacts of Ca2+ supplementation in alginate-dominated biofilms grown in vitro, and we evaluate the impact of targeted enzyme treatments on clearance by immune cells. We use multiple-particle tracking microrheology to evaluate the changes in biofilm viscoelasticity caused by treatment with alginate lyase or DNase I. For biofilms grown without Ca2+, we correlate a decrease in relative elasticity with increased phagocytic success. However, we find that growth with Ca2+ supplementation disrupts this correlation except in the case where both enzymes are applied. This suggests that the calcium cation may be impacting the microstructure of the biofilm in nontrivial ways. Indeed, confocal laser scanning fluorescence microscopy and scanning electron microscopy reveal unique Ca2+-dependent eDNA and alginate microstructures. Our results suggest that the presence of Ca2+ drives the formation of structurally and compositionally discrete microdomains within the biofilm through electrostatic interactions with the anionic matrix components eDNA and alginate. Further, we observe that these structures serve a protective function as the dissolution of both components is required to render biofilm bacteria vulnerable to phagocytosis by neutrophils.
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Affiliation(s)
- Marilyn J. Wells
- Department of Physics, The University of Texas at Austin, 2515 Speedway, C1600, Austin, Texas 78712-1192, USA
- Center for Nonlinear Dynamics, The University of Texas at Austin, 2515 Speedway, Stop C1610, Austin, Texas 78712-11993, USA
| | - Hailey Currie
- Department of Physics, The University of Texas at Austin, 2515 Speedway, C1600, Austin, Texas 78712-1192, USA
- Center for Nonlinear Dynamics, The University of Texas at Austin, 2515 Speedway, Stop C1610, Austin, Texas 78712-11993, USA
| | - Vernita D. Gordon
- Department of Physics, The University of Texas at Austin, 2515 Speedway, C1600, Austin, Texas 78712-1192, USA
- Center for Nonlinear Dynamics, The University of Texas at Austin, 2515 Speedway, Stop C1610, Austin, Texas 78712-11993, USA
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Norman Hackerman Building, 100 East 24th St., NHB 4500, Austin, Texas 78712, USA
- LaMontagne Center for Infectious Disease, The University of Texas at Austin, Neural Molecular Science Building, 2506 Speedway, Stop A5000, Austin, Texas 78712, USA
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20
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Madan V, Albacete‐Albacete L, Jin L, Scaturro P, Watson JL, Muschalik N, Begum F, Boulanger J, Bauer K, Kiebler MA, Derivery E, Bullock SL. HEATR5B associates with dynein-dynactin and promotes motility of AP1-bound endosomal membranes. EMBO J 2023; 42:e114473. [PMID: 37872872 PMCID: PMC10690479 DOI: 10.15252/embj.2023114473] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/25/2023] Open
Abstract
The microtubule motor dynein mediates polarised trafficking of a wide variety of organelles, vesicles and macromolecules. These functions are dependent on the dynactin complex, which helps recruit cargoes to dynein's tail and activates motor movement. How the dynein-dynactin complex orchestrates trafficking of diverse cargoes is unclear. Here, we identify HEATR5B, an interactor of the adaptor protein-1 (AP1) clathrin adaptor complex, as a novel player in dynein-dynactin function. HEATR5B was recovered in a biochemical screen for proteins whose association with the dynein tail is augmented by dynactin. We show that HEATR5B binds directly to the dynein tail and dynactin and stimulates motility of AP1-associated endosomal membranes in human cells. We also demonstrate that the Drosophila HEATR5B homologue is an essential gene that selectively promotes dynein-based transport of AP1-bound membranes to the Golgi apparatus. As HEATR5B lacks the coiled-coil architecture typical of dynein adaptors, our data point to a non-canonical process orchestrating motor function on a specific cargo. We additionally show that HEATR5B promotes association of AP1 with endosomal membranes independently of dynein. Thus, HEATR5B co-ordinates multiple events in AP1-based trafficking.
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Affiliation(s)
- Vanesa Madan
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
- Present address:
AbcamCambridgeUK
| | - Lucas Albacete‐Albacete
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Li Jin
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | | | - Joseph L Watson
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Nadine Muschalik
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Farida Begum
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Jérôme Boulanger
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Karl Bauer
- Biomedical Center, Department for Cell Biology, Medical FacultyLudwig‐Maximilians‐University of MunichMunichGermany
| | - Michael A Kiebler
- Biomedical Center, Department for Cell Biology, Medical FacultyLudwig‐Maximilians‐University of MunichMunichGermany
| | - Emmanuel Derivery
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
| | - Simon L Bullock
- Division of Cell BiologyMedical Research Council (MRC) Laboratory of Molecular BiologyCambridgeUK
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21
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Yuan Y, Wang X, Jin J, Tang Z, Xian W, Zhang X, Fu J, He K, Liu X. The Salmonella Typhimurium Effector SpvB Subverts Host Membrane Trafficking by Targeting Clathrin and AP-1. Mol Cell Proteomics 2023; 22:100674. [PMID: 37924977 PMCID: PMC10696399 DOI: 10.1016/j.mcpro.2023.100674] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/21/2023] [Accepted: 11/01/2023] [Indexed: 11/06/2023] Open
Abstract
Salmonella enterica, the etiological agent of gastrointestinal and systemic diseases, translocates a plethora of virulence factors through its type III secretion systems to host cells during infection. Among them, SpvB has been reported to harbor an ADP-ribosyltransferase domain in its C terminus, which destabilizes host cytoskeleton by modifying actin. However, whether this effector targets other host factors as well as the function of its N terminus still remains to be determined. Here, we found that SpvB targets clathrin and its adaptor AP-1 (adaptor protein 1) via interactions with its N-terminal domain. Notably, our data suggest that SpvB-clathrin/AP-1 associations disrupt clathrin-mediated endocytosis and protein secretion pathway as well. In addition, knocking down of AP-1 promotes Salmonella intracellular survival and proliferation in host cells.
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Affiliation(s)
- Yi Yuan
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xinghao Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jie Jin
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Zhiheng Tang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Wei Xian
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xinyi Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jiaqi Fu
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Zoonotic Diseases, The First Hospital of Jilin University, Changchun, China.
| | - Kangmin He
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China.
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22
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DiRusso CJ, DeMaria AM, Wong J, Wang W, Jordanides JJ, Whitty A, Allen KN, Gilmore TD. A conserved core region of the scaffold NEMO is essential for signal-induced conformational change and liquid-liquid phase separation. J Biol Chem 2023; 299:105396. [PMID: 37890781 PMCID: PMC10694592 DOI: 10.1016/j.jbc.2023.105396] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Scaffold proteins help mediate interactions between protein partners, often to optimize intracellular signaling. Herein, we use comparative, biochemical, biophysical, molecular, and cellular approaches to investigate how the scaffold protein NEMO contributes to signaling in the NF-κB pathway. Comparison of NEMO and the related protein optineurin from a variety of evolutionarily distant organisms revealed that a central region of NEMO, called the Intervening Domain (IVD), is conserved between NEMO and optineurin. Previous studies have shown that this central core region of the IVD is required for cytokine-induced activation of IκB kinase (IKK). We show that the analogous region of optineurin can functionally replace the core region of the NEMO IVD. We also show that an intact IVD is required for the formation of disulfide-bonded dimers of NEMO. Moreover, inactivating mutations in this core region abrogate the ability of NEMO to form ubiquitin-induced liquid-liquid phase separation droplets in vitro and signal-induced puncta in vivo. Thermal and chemical denaturation studies of truncated NEMO variants indicate that the IVD, while not intrinsically destabilizing, can reduce the stability of surrounding regions of NEMO due to the conflicting structural demands imparted on this region by flanking upstream and downstream domains. This conformational strain in the IVD mediates allosteric communication between the N- and C-terminal regions of NEMO. Overall, these results support a model in which the IVD of NEMO participates in signal-induced activation of the IKK/NF-κB pathway by acting as a mediator of conformational changes in NEMO.
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Affiliation(s)
| | - Anthony M DeMaria
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Judy Wong
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Wei Wang
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Jack J Jordanides
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, Massachusetts, USA.
| | - Thomas D Gilmore
- Department of Biology, Boston University, Boston, Massachusetts, USA.
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23
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Camargo LDN, Righetti RF, de Almeida FM, dos Santos TM, Fukuzaki S, Martins NAB, Barbeiro MC, Saraiva-Romanholo BM, Lopes FDTQDS, Leick EA, Prado CM, Tibério IDFLC. Modulating asthma-COPD overlap responses with IL-17 inhibition. Front Immunol 2023; 14:1271342. [PMID: 37965351 PMCID: PMC10641519 DOI: 10.3389/fimmu.2023.1271342] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Background IL-17 is a modulator of the inflammatory response and is implicated in lung remodeling in both asthma and chronic obstructive pulmonary disease (COPD). Well as and probably in patients with asthma-COPD overlap (ACO). Methods In this study, we evaluated the response of the airways and alveolar septa to anti-IL-17 treatment in an ACO model. Fifty-six male BALB/c mice were sensitized with ovalbumin (OVA group), received porcine pancreatic elastase (PPE group), or both (ACO group). Mice were then treated with either anti-IL-17 monoclonal antibody or saline. We evaluated hyperresponsiveness, bronchoalveolar lavage fluid (BALF) cell counts, and mean alveolar diameter. We quantified inflammatory, response, extracellular matrix remodeling, oxidative stress markers, and signaling pathway markers. Results Anti-IL-17 treatment in the ACO anti-IL-17 group reduced the maximum response of respiratory system Rrs, Ers, Raw, Gtis, this when compared to the ACO group (p<0.05). There was a reduction in the total number of inflammatory cells, neutrophils, and macrophages in the BALF in the ACO anti-IL-17 group compared to the ACO group (p<0.05). There was attenuated dendritic cells, CD4+, CD8+, FOXP3, IL-1β, IL-2, IL-6, IL-13, IL-17, IL-33 in ACO anti-IL-17 group in airway and alveolar septum compared to the ACO group (p<0.05). We observed a reduction of MMP-9, MMP-12, TIMP-1, TGF-β, collagen type I in ACO anti-IL-17 group in airway and alveolar septum compared to the ACO group (p < 0.05). We also observed a reduction of iNOS and 8-iso-PGF2α in the airways and in the alveolar septum was reduced in the ACO anti-IL-17group compared to the ACO group (p < 0.05). Regarding the signaling pathways, NF-kB, ROCK-1, and ROCK-2 in the airway and alveolar septum were attenuated in the ACO anti-IL-17 group when compared to the ACO group (p<0.05). Conclusions Our results suggest that inhibiting IL-17 modulates cell-associated cytokine production in lung tissue, extracellular matrix remodeling, and oxidative stress in ACO through the modulation of NF-kB and FOXP3.
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Affiliation(s)
- Leandro do Nascimento Camargo
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
- Serviço de Reabilitação, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Renato Fraga Righetti
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
- Serviço de Reabilitação, Hospital Sírio-Libanês, São Paulo, Brazil
| | | | - Tabata Maruyama dos Santos
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
- Serviço de Reabilitação, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Silvia Fukuzaki
- Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | | | | | - Carla Máximo Prado
- Department of Bioscience, Federal University of São Paulo, Santos, São Paulo, Brazil
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24
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Wells MJ, Currie H, Gordon VD. Physiological concentrations of calcium interact with alginate and extracellular DNA in the matrices of Pseudomonas aeruginosa biofilms to impede phagocytosis by neutrophils. bioRxiv 2023:2023.10.23.563605. [PMID: 37961083 PMCID: PMC10634743 DOI: 10.1101/2023.10.23.563605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Biofilms are communities of interacting microbes embedded in a matrix of polymer, protein, and other materials. Biofilms develop distinct mechanical characteristics that depend on their predominant matrix components. These matrix components may be produced by microbes themselves or, for infections in vivo, incorporated from the host environment. Pseudomonas aeruginosa is a human pathogen that forms robust biofilms that extensively tolerate antibiotics and effectively evade clearance by the immune system. Two of the important bacterial-produced polymers in the matrices of P. aeruginosa biofilms are alginate and extracellular DNA (eDNA), both of which are anionic and therefore have the potential to interact electrostatically with cations. Many physiological sites of infection contain significant concentrations of the calcium ion (Ca2+). In this study we investigate the structural and mechanical impacts of Ca2+ supplementation in alginate-dominated biofilms grown in vitro and we evaluate the impact of targeted enzyme treatments on clearance by immune cells. We use multiple particle tracking microrheology to evaluate the changes in biofilm viscoelasticity caused by treatment with alginate lyase and/or DNAse I. For biofilms grown without Ca2+, we correlate a decrease in relative elasticity with increased phagocytic success. However, we find that growth with Ca2+ supplementation disrupts this correlation except in the case where both enzymes are applied. This suggests that the calcium cation may be impacting the microstructure of the biofilm in non-trivial ways. Indeed, confocal laser scanning fluorescence microscopy and scanning electron microscopy reveal unique Ca2+-dependent eDNA and alginate microstructures. Our results suggest that the presence of Ca2+ drives the formation of structurally and compositionally discrete microdomains within the biofilm through electrostatic interactions with the anionic matrix components eDNA and alginate. Further, we observe that these structures serve a protective function as the dissolution of both components is required to render biofilm bacteria vulnerable to phagocytosis by neutrophils.
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Affiliation(s)
- Marilyn J. Wells
- Department of Physics, The University of Texas at Austin, 2515 Speedway, C1600, Austin, Texas 78712-1192, USA
- Center for Nonlinear Dynamics, The University of Texas at Austin, 2515 Speedway, Stop C1610, Austin, Texas 78712-11993, USA
| | - Hailey Currie
- Department of Physics, The University of Texas at Austin, 2515 Speedway, C1600, Austin, Texas 78712-1192, USA
- Center for Nonlinear Dynamics, The University of Texas at Austin, 2515 Speedway, Stop C1610, Austin, Texas 78712-11993, USA
| | - Vernita D. Gordon
- Department of Physics, The University of Texas at Austin, 2515 Speedway, C1600, Austin, Texas 78712-1192, USA
- Center for Nonlinear Dynamics, The University of Texas at Austin, 2515 Speedway, Stop C1610, Austin, Texas 78712-11993, USA
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Norman Hackerman Building, 100 East 24th St., NHB 4500, Austin, Texas 78712, USA
- LaMontagne Center for Infectious Disease, The University of Texas at Austin, Neural Molecular Science Building, 2506 Speedway, Stop A5000, Austin, Texas 78712, USA
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25
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Fischer TD, Bunker EN, Zhu PP, Le Guerroué F, Dominguez-Martin E, Scavone F, Cohen R, Yao T, Wang Y, Werner A, Youle RJ. STING induces LUBAC-mediated synthesis of linear ubiquitin chains to stimulate innate immune signaling. bioRxiv 2023:2023.10.14.562349. [PMID: 37873486 PMCID: PMC10592814 DOI: 10.1101/2023.10.14.562349] [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] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
STING activation by cyclic dinucleotides in mammals induces interferon- and NFκB -related gene expression, and the lipidation of LC3B at Golgi membranes. While mechanisms of the interferon response are well understood, the mechanisms of NFκB activation mediated by STING remain unclear. We report that STING activation induces K63- and M1-linked/linear ubiquitin chain formation at LC3B-associated Golgi membranes. Loss of the LUBAC E3 ubiquitin ligase prevents formation of linear, but not K63-linked ubiquitin chains or STING activation and inhibits STING-induced NFκB and IRF3-mediated signaling in monocytic THP1 cells. The proton channel activity of STING is also important for both K63 and linear ubiquitin chain formation, and NFκB- and interferon-related gene expression. Thus, LUBAC synthesis of linear ubiquitin chains regulates STING-mediated innate immune signaling.
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Affiliation(s)
- Tara D. Fischer
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - Eric N. Bunker
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - Peng-Peng Zhu
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - François Le Guerroué
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - Eunice Dominguez-Martin
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - Francesco Scavone
- Department of Biochemistry and Molecular Biology, Colorado State University; Fort Collins, CO, USA
| | - Robert Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University; Fort Collins, CO, USA
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University; Fort Collins, CO, USA
| | - Yan Wang
- Mass Spectrometry, National Institute of Dental and Craniofacial Research, National Institutes of Health; Bethesda, MD, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health; Bethesda, MD, USA
| | - Richard J. Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
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26
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Sun Y, Chen J, Pommier Y. Real-time imaging of drug-induced trapping of cellular topoisomerases and poly(ADP-ribose) polymerase 1 at the single-molecule level. Nucleic Acids Res 2023; 51:e97. [PMID: 37670571 PMCID: PMC10570045 DOI: 10.1093/nar/gkad735] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/29/2023] [Accepted: 08/26/2023] [Indexed: 09/07/2023] Open
Abstract
Topoisomerases (TOP1, TOP2α, and β) are nuclear enzymes crucial for virtually all aspects of DNA metabolisms. They also are the targets of important anti-tumor chemotherapeutics that act by trapping the otherwise reversible topoisomerase-DNA covalent complex intermediates (TOPccs) that are formed during their catalytic reactions, resulting in long-lived topoisomerase DNA-protein crosslinks (TOP-DPCs) that interfere with DNA transactions. The Poly(ADP-ribose) polymerase (PARP) family protein PARP1 is activated by DNA damage to recruit DNA repair proteins, and PARP inhibitors are another class of commonly used chemotherapeutics, which bind and trap PARP molecules on DNA. To date, the trapping of TOPccs and PARP by their respective inhibitors can only be measured by immune-biochemical methods in cells. Here, we developed an imaging-based approach enabling real-time monitoring of drug-induced trapping of TOPccs and PARP1 in live cells at the single-molecule level. Capitalizing on this approach, we calculated the fraction of self-fluorescence tag-labeled topoisomerases and PARP single-molecules that are trapped by their respective inhibitors in real time. This novel technique should help elucidate the molecular processes that repair TOPcc and PARP trapping and facilitate the development of novel topoisomerase and PARP inhibitor-based therapies.
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Affiliation(s)
- Yilun Sun
- Laboratory of Molecular Pharmacology and Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy (AIM) Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology and Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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27
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Watson JL, Krüger LK, Ben-Sasson AJ, Bittleston A, Shahbazi MN, Planelles-Herrero VJ, Chambers JE, Manton JD, Baker D, Derivery E. Synthetic Par polarity induces cytoskeleton asymmetry in unpolarized mammalian cells. Cell 2023; 186:4710-4727.e35. [PMID: 37774705 PMCID: PMC10765089 DOI: 10.1016/j.cell.2023.08.034] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/04/2023] [Accepted: 08/25/2023] [Indexed: 10/01/2023]
Abstract
Polarized cells rely on a polarized cytoskeleton to function. Yet, how cortical polarity cues induce cytoskeleton polarization remains elusive. Here, we capitalized on recently established designed 2D protein arrays to ectopically engineer cortical polarity of virtually any protein of interest during mitosis in various cell types. This enables direct manipulation of polarity signaling and the identification of the cortical cues sufficient for cytoskeleton polarization. Using this assay, we dissected the logic of the Par complex pathway, a key regulator of cytoskeleton polarity during asymmetric cell division. We show that cortical clustering of any Par complex subunit is sufficient to trigger complex assembly and that the primary kinetic barrier to complex assembly is the relief of Par6 autoinhibition. Further, we found that inducing cortical Par complex polarity induces two hallmarks of asymmetric cell division in unpolarized mammalian cells: spindle orientation, occurring via Par3, and central spindle asymmetry, depending on aPKC activity.
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Affiliation(s)
- Joseph L Watson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Lara K Krüger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Ariel J Ben-Sasson
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alice Bittleston
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Marta N Shahbazi
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | | | - Joseph E Chambers
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Hills Rd, Cambridge, UK
| | - James D Manton
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Emmanuel Derivery
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
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28
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Cao F, Deliz‐Aguirre R, Gerpott FHU, Ziska E, Taylor MJ. Myddosome clustering in IL-1 receptor signaling regulates the formation of an NF-kB activating signalosome. EMBO Rep 2023; 24:e57233. [PMID: 37602973 PMCID: PMC10561168 DOI: 10.15252/embr.202357233] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/24/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023] Open
Abstract
IL-1 receptor (IL-1R) signaling can activate thresholded invariant outputs and proportional outputs that scale with the amount of stimulation. Both responses require the Myddosome, a multiprotein complex. The Myddosome is required for polyubiquitin chain formation and NF-kB signaling. However, how these signals are spatially and temporally regulated to drive switch-like and proportional outcomes is not understood. During IL-1R signaling, Myddosomes dynamically reorganize into multi-Myddosome clusters at the cell membrane. Blockade of clustering using nanoscale extracellular barriers reduces NF-kB activation. Myddosomes function as scaffolds that assemble an NF-kB signalosome consisting of E3-ubiquitin ligases TRAF6 and LUBAC, K63/M1-linked polyubiquitin chains, phospho-IKK, and phospho-p65. This signalosome preferentially assembles at regions of high Myddosome density, which enhances the recruitment of TRAF6 and LUBAC. Extracellular barriers that restrict Myddosome clustering perturbed the recruitment of both ligases. We find that LUBAC was especially sensitive to clustering with 10-fold lower recruitment to single Myddosomes than clustered Myddosomes. These data reveal that the clustering behavior of Myddosomes provides a basis for digital and analog IL-1R signaling.
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Affiliation(s)
- Fakun Cao
- Max Planck Institute for Infection BiologyBerlinGermany
| | | | | | - Elke Ziska
- Max Planck Institute for Infection BiologyBerlinGermany
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29
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Harding O, Holzer E, Riley JF, Martens S, Holzbaur ELF. Damaged mitochondria recruit the effector NEMO to activate NF-κB signaling. Mol Cell 2023; 83:3188-3204.e7. [PMID: 37683611 PMCID: PMC10510730 DOI: 10.1016/j.molcel.2023.08.005] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 05/25/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
Failure to clear damaged mitochondria via mitophagy disrupts physiological function and may initiate damage signaling via inflammatory cascades, although how these pathways intersect remains unclear. We discovered that nuclear factor kappa B (NF-κB) essential regulator NF-κB effector molecule (NEMO) is recruited to damaged mitochondria in a Parkin-dependent manner in a time course similar to recruitment of the structurally related mitophagy adaptor, optineurin (OPTN). Upon recruitment, NEMO partitions into phase-separated condensates distinct from OPTN but colocalizing with p62/SQSTM1. NEMO recruitment, in turn, recruits the active catalytic inhibitor of kappa B kinase (IKK) component phospho-IKKβ, initiating NF-κB signaling and the upregulation of inflammatory cytokines. Consistent with a potential neuroinflammatory role, NEMO is recruited to mitochondria in primary astrocytes upon oxidative stress. These findings suggest that damaged, ubiquitinated mitochondria serve as an intracellular platform to initiate innate immune signaling, promoting the formation of activated IKK complexes sufficient to activate NF-κB signaling. We propose that mitophagy and NF-κB signaling are initiated as parallel pathways in response to mitochondrial stress.
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Affiliation(s)
- Olivia Harding
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Elisabeth Holzer
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA; Max Perutz Labs, Vienna Biocenter Campus, Vienna, Austria; Center for Molecular Biology, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria; Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Julia F Riley
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sascha Martens
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA; Max Perutz Labs, Vienna Biocenter Campus, Vienna, Austria; Center for Molecular Biology, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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30
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Fivenson EM, Rohs PDA, Vettiger A, Sardis MF, Torres G, Forchoh A, Bernhardt TG. A role for the Gram-negative outer membrane in bacterial shape determination. Proc Natl Acad Sci U S A 2023; 120:e2301987120. [PMID: 37607228 PMCID: PMC10469335 DOI: 10.1073/pnas.2301987120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 02/03/2023] [Accepted: 07/21/2023] [Indexed: 08/24/2023] Open
Abstract
The cell envelope of Gram-negative bacteria consists of three distinct layers: the cytoplasmic membrane, a cell wall made of peptidoglycan (PG), and an asymmetric outer membrane (OM) composed of phospholipid in the inner leaflet and lipopolysaccharide (LPS) glycolipid in the outer leaflet. The PG layer has long been thought to be the major structural component of the envelope protecting cells from osmotic lysis and providing them with their characteristic shape. In recent years, the OM has also been shown to be a load-bearing layer of the cell surface that fortifies cells against internal turgor pressure. However, whether the OM also plays a role in morphogenesis has remained unclear. Here, we report that changes in LPS synthesis or modification predicted to strengthen the OM can suppress the growth and shape defects of Escherichia coli mutants with reduced activity in a conserved PG synthesis machine called the Rod complex (elongasome) that is responsible for cell elongation and shape determination. Evidence is presented that OM fortification in the shape mutants restores the ability of MreB cytoskeletal filaments to properly orient the synthesis of new cell wall material by the Rod complex. Our results are therefore consistent with a role for the OM in the propagation of rod shape during growth in addition to its well-known function as a diffusion barrier promoting the intrinsic antibiotic resistance of Gram-negative bacteria.
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Affiliation(s)
- Elayne M. Fivenson
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Patricia D. A. Rohs
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Andrea Vettiger
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Marios F. Sardis
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Grasiela Torres
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Alison Forchoh
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Thomas G. Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- HHMI, Chevy Chase, MD20815
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31
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Sexton T, Platania A, Erb C, Barbieri M, Molcrette B, Grandgirard E, de Kort M, Meabum K, Taylor T, Shchuka V, Kocanova S, Oliveira G, Mitchell J, Soutoglou E, Lenstra T, Molina N, Papantonis A, Bystricky K. Competition between transcription and loop extrusion modulates promoter and enhancer dynamics. Res Sq 2023:rs.3.rs-3164817. [PMID: 37645793 PMCID: PMC10462181 DOI: 10.21203/rs.3.rs-3164817/v1] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The spatiotemporal configuration of genes with distal regulatory elements, and the impact of chromatin mobility on transcription, remain unclear. Loop extrusion is an attractive model for bringing genetic elements together, but how this functionally interacts with transcription is also largely unknown. We combine live tracking of genomic loci and nascent transcripts with molecular dynamics simulations to assess the spatiotemporal arrangement of the Sox2 gene and its enhancer, in response to a battery of perturbations. We find a close link between chromatin mobility and transcriptional status: active elements display more constrained mobility, consistent with confinement within specialized nuclear sites, and alterations in enhancer mobility distinguish poised from transcribing alleles. Strikingly, we find that whereas loop extrusion and transcription factor-mediated clustering contribute to promoter-enhancer proximity, they have antagonistic effects on chromatin dynamics. This provides an experimental framework for the underappreciated role of chromatin dynamics in genome regulation.
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Affiliation(s)
- Tom Sexton
- IGBMC (Institute of Genetics and Molecular and Cellular Biology)
| | | | - Cathie Erb
- IGBMC (Institute of Genetics and Molecular and Cellular Biology)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Nacho Molina
- IGBMC (Institute of Genetics and Molecular and Cellular Biology)
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32
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Hardiman W, Clark M, Friel C, Huett A, Pérez-Cota F, Setchfield K, Wright AJ, Tassieri M. Living cells as a biological analog of optical tweezers - a non-invasive microrheology approach. Acta Biomater 2023; 166:317-325. [PMID: 37137402 DOI: 10.1016/j.actbio.2023.04.039] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/14/2023] [Accepted: 04/25/2023] [Indexed: 05/05/2023]
Abstract
Microrheology, the study of fluids on micron length-scales, promises to reveal insights into cellular biology, including mechanical biomarkers of disease and the interplay between biomechanics and cellular function. Here a minimally-invasive passive microrheology technique is applied to individual living cells by chemically binding a bead to the surface of a cell, and observing the mean squared displacement of the bead at timescales ranging from milliseconds to 100s of seconds. Measurements are repeated over the course of hours, and presented alongside analysis to quantify changes in the cells' low-frequency elastic modulus, G0', and the cell's dynamics over the time window ∼10-2 s to 10 s. An analogy to optical trapping allows verification of the invariant viscosity of HeLa S3 cells under control conditions and after cytoskeletal disruption. Stiffening of the cell is observed during cytoskeletal rearrangement in the control case, and cell softening when the actin cytoskeleton is disrupted by Latrunculin B. These data correlate with conventional understanding that integrin binding and recruitment triggers cytoskeletal rearrangement. This is, to our knowledge, the first time that cell stiffening has been measured during focal adhesion maturation, and the longest time over which such stiffening has been quantified by any means. STATEMENT OF SIGNIFICANCE: Here, we present an approach for studying mechanical properties of live cells without applying external forces or inserting tracers. Regulation of cellular biomechanics is crucial to healthy cell function. For the first time in literature, we can non-invasively and passively quantify cell mechanics during interactions with functionalised surface. Our method can monitor the maturation of adhesion sites on the surface of individual live cells without disrupting the cell mechanics by applying forces to the cell. We observe a stiffening response in cells over tens of minutes after a bead chemically binds. This stiffening reduces the deformation rate of the cytoskeleton, although the internal force generation increases. Our method has potential for applications to study mechanics during cell-surface and cell-vesicle interactions.
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Affiliation(s)
- William Hardiman
- Optics and Photonics Research Group, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Matt Clark
- Optics and Photonics Research Group, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK
| | - Claire Friel
- School of Life Sciences, University of Nottingham, Medical School, QMC, Nottingham NG7 2UH, UK
| | - Alan Huett
- School of Life Sciences, University of Nottingham, Medical School, QMC, Nottingham NG7 2UH, UK
| | - Fernando Pérez-Cota
- Optics and Photonics Research Group, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK
| | - Kerry Setchfield
- Optics and Photonics Research Group, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK
| | - Amanda J Wright
- Optics and Photonics Research Group, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Manlio Tassieri
- Division of Biomedical Engineering, James Watt School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK.
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Yaganoglu S, Kalyviotis K, Vagena-Pantoula C, Jülich D, Gaub BM, Welling M, Lopes T, Lachowski D, Tang SS, Del Rio Hernandez A, Salem V, Müller DJ, Holley SA, Vermot J, Shi J, Helassa N, Török K, Pantazis P. Highly specific and non-invasive imaging of Piezo1-dependent activity across scales using GenEPi. Nat Commun 2023; 14:4352. [PMID: 37468521 PMCID: PMC10356793 DOI: 10.1038/s41467-023-40134-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 07/18/2022] [Accepted: 07/11/2023] [Indexed: 07/21/2023] Open
Abstract
Mechanosensing is a ubiquitous process to translate external mechanical stimuli into biological responses. Piezo1 ion channels are directly gated by mechanical forces and play an essential role in cellular mechanotransduction. However, readouts of Piezo1 activity are mainly examined by invasive or indirect techniques, such as electrophysiological analyses and cytosolic calcium imaging. Here, we introduce GenEPi, a genetically-encoded fluorescent reporter for non-invasive optical monitoring of Piezo1-dependent activity. We demonstrate that GenEPi has high spatiotemporal resolution for Piezo1-dependent stimuli from the single-cell level to that of the entire organism. GenEPi reveals transient, local mechanical stimuli in the plasma membrane of single cells, resolves repetitive contraction-triggered stimulation of beating cardiomyocytes within microtissues, and allows for robust and reliable monitoring of Piezo1-dependent activity in vivo. GenEPi will enable non-invasive optical monitoring of Piezo1 activity in mechanochemical feedback loops during development, homeostatic regulation, and disease.
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Affiliation(s)
- Sine Yaganoglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | | | | | - Dörthe Jülich
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Benjamin M Gaub
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Maaike Welling
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
- Department of Bioengineering, Imperial College London, London, UK
| | - Tatiana Lopes
- Section of Investigative Medicine, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | | | - See Swee Tang
- Department of Bioengineering, Imperial College London, London, UK
| | | | - Victoria Salem
- Department of Bioengineering, Imperial College London, London, UK
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Scott A Holley
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Julien Vermot
- Department of Bioengineering, Imperial College London, London, UK
| | - Jian Shi
- Leeds Institute of Cardiovascular and Metabolic Medicine, LIGHT Laboratories, University of Leeds, Leeds, UK
| | - Nordine Helassa
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Katalin Török
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
| | - Periklis Pantazis
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland.
- Department of Bioengineering, Imperial College London, London, UK.
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34
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Broadbent DG, Barnaba C, Perez GI, Schmidt JC. Quantitative analysis of autophagy reveals the role of ATG9 and ATG2 in autophagosome formation. J Cell Biol 2023; 222:e202210078. [PMID: 37115157 PMCID: PMC10148237 DOI: 10.1083/jcb.202210078] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [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: 10/18/2022] [Revised: 02/03/2023] [Accepted: 03/17/2023] [Indexed: 04/29/2023] Open
Abstract
Autophagy is a catabolic pathway required for the recycling of cytoplasmic materials. To define the mechanisms underlying autophagy it is critical to quantitatively characterize the dynamic behavior of autophagy factors in living cells. Using a panel of cell lines expressing HaloTagged autophagy factors from their endogenous loci, we analyzed the abundance, single-molecule dynamics, and autophagosome association kinetics of autophagy proteins involved in autophagosome biogenesis. We demonstrate that autophagosome formation is inefficient and ATG2-mediated tethering to donor membranes is a key commitment step in autophagosome formation. Furthermore, our observations support the model that phagophores are initiated by the accumulation of autophagy factors on mobile ATG9 vesicles, and that the ULK1 complex and PI3-kinase form a positive feedback loop required for autophagosome formation. Finally, we demonstrate that the duration of autophagosome biogenesis is ∼110 s. In total, our work provides quantitative insight into autophagosome biogenesis and establishes an experimental framework to analyze autophagy in human cells.
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Affiliation(s)
- David G. Broadbent
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Carlo Barnaba
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Gloria I. Perez
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Jens C. Schmidt
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Obstetrics and Gynecology, Michigan State University, East Lansing, MI, USA
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35
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Sun Y, Baechler SA, Zhang X, Kumar S, Factor VM, Arakawa Y, Chau CH, Okamoto K, Parikh A, Walker B, Su YP, Chen J, Ting T, Huang SYN, Beck E, Itkin Z, McKnight C, Xie C, Roper N, Nijhawan D, Figg WD, Meltzer PS, Yang JC, Thomas CJ, Pommier Y. Targeting neddylation sensitizes colorectal cancer to topoisomerase I inhibitors by inactivating the DCAF13-CRL4 ubiquitin ligase complex. Nat Commun 2023; 14:3762. [PMID: 37353483 PMCID: PMC10290057 DOI: 10.1038/s41467-023-39374-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 04/02/2022] [Accepted: 06/09/2023] [Indexed: 06/25/2023] Open
Abstract
Colorectal cancers (CRCs) are prevalent worldwide, yet current treatments remain inadequate. Using chemical genetic screens, we identify that co-inhibition of topoisomerase I (TOP1) and NEDD8 is synergistically cytotoxic in human CRC cells. Combination of the TOP1 inhibitor irinotecan or its bioactive metabolite SN38 with the NEDD8-activating enzyme inhibitor pevonedistat exhibits synergy in CRC patient-derived organoids and xenografts. Mechanistically, we show that pevonedistat blocks the ubiquitin/proteasome-dependent repair of TOP1 DNA-protein crosslinks (TOP1-DPCs) induced by TOP1 inhibitors and that the CUL4-RBX1 complex (CRL4) is a prominent ubiquitin ligase acting on TOP1-DPCs for proteasomal degradation upon auto-NEDD8 modification during replication. We identify DCAF13, a DDB1 and Cullin Associated Factor, as the receptor of TOP1-DPCs for CRL4. Our study not only uncovers a replication-coupled ubiquitin-proteasome pathway for the repair of TOP1-DPCs but also provides molecular and translational rationale for combining TOP1 inhibitors and pevonedistat for CRC and other types of cancers.
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Affiliation(s)
- Yilun Sun
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Simone A Baechler
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xiaohu Zhang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Suresh Kumar
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Valentina M Factor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yasuhiro Arakawa
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cindy H Chau
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kanako Okamoto
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anup Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bob Walker
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yijun P Su
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tabitha Ting
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Shar-Yin N Huang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Erin Beck
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Zina Itkin
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Crystal McKnight
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Changqing Xie
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nitin Roper
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Deepak Nijhawan
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - William Douglas Figg
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - James C Yang
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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36
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Beiza-Canelo N, Moulle H, Pujol T, Panier T, Migault G, Le Goc G, Tapie P, Desprat N, Straka H, Debrégeas G, Bormuth V. Magnetic actuation of otoliths allows behavioral and brain-wide neuronal exploration of vestibulo-motor processing in larval zebrafish. Curr Biol 2023:S0960-9822(23)00621-8. [PMID: 37285844 DOI: 10.1016/j.cub.2023.05.026] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/23/2022] [Accepted: 05/11/2023] [Indexed: 06/09/2023]
Abstract
The vestibular system in the inner ear plays a central role in sensorimotor control by informing the brain about the orientation and acceleration of the head. However, most experiments in neurophysiology are performed using head-fixed configurations, depriving animals of vestibular inputs. To overcome this limitation, we decorated the utricular otolith of the vestibular system in larval zebrafish with paramagnetic nanoparticles. This procedure effectively endowed the animal with magneto-sensitive capacities: applied magnetic field gradients induced forces on the otoliths, resulting in robust behavioral responses comparable to those evoked by rotating the animal by up to 25°. We recorded the whole-brain neuronal response to this fictive motion stimulation using light-sheet functional imaging. Experiments performed in unilaterally injected fish revealed the activation of a commissural inhibition between the brain hemispheres. This magnetic-based stimulation technique for larval zebrafish opens new perspectives to functionally dissect the neural circuits underlying vestibular processing and to develop multisensory virtual environments, including vestibular feedback.
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Affiliation(s)
- Natalia Beiza-Canelo
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Hippolyte Moulle
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Thomas Pujol
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France; IBENS, Département de Biologie, École Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France
| | - Thomas Panier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France; Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Plateforme d'Imagerie, 75005 Paris, France
| | - Geoffrey Migault
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Guillaume Le Goc
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Pierre Tapie
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Nicolas Desprat
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, 75005 Paris, France; Université Paris Diderot, 10 Rue Alice Domon et Leonie Duquet, 75013 Paris, France
| | - Hans Straka
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshadernerstr. 2, 82152 Planegg, Germany
| | - Georges Debrégeas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Volker Bormuth
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France.
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37
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DiRusso CJ, DeMaria AM, Wong J, Jordanides JJ, Whitty A, Allen KN, Gilmore TD. A Conserved Core Region of the Scaffold NEMO is Essential for Signal-induced Conformational Change and Liquid-liquid Phase Separation. bioRxiv 2023:2023.05.25.542299. [PMID: 37292615 PMCID: PMC10245932 DOI: 10.1101/2023.05.25.542299] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Scaffold proteins help mediate interactions between protein partners, often to optimize intracellular signaling. Herein, we use comparative, biochemical, biophysical, molecular, and cellular approaches to investigate how the scaffold protein NEMO contributes to signaling in the NF-κB pathway. Comparison of NEMO and the related protein optineurin from a variety of evolutionarily distant organisms revealed that a central region of NEMO, called the Intervening Domain (IVD), is conserved between NEMO and optineurin. Previous studies have shown that this central core region of the IVD is required for cytokine-induced activation of IκB kinase (IKK). We show that the analogous region of optineurin can functionally replace the core region of the NEMO IVD. We also show that an intact IVD is required for the formation of disulfide-bonded dimers of NEMO. Moreover, inactivating mutations in this core region abrogate the ability of NEMO to form ubiquitin-induced liquid-liquid phase separation droplets in vitro and signal-induced puncta in vivo. Thermal and chemical denaturation studies of truncated NEMO variants indicate that the IVD, while not intrinsically destabilizing, can reduce the stability of surrounding regions of NEMO, due to the conflicting structural demands imparted on this region by flanking upstream and downstream domains. This conformational strain in the IVD mediates allosteric communication between N- and C-terminal regions of NEMO. Overall, these results support a model in which the IVD of NEMO participates in signal-induced activation of the IKK/NF-κB pathway by acting as a mediator of conformational changes in NEMO.
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Affiliation(s)
| | | | - Judy Wong
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Karen N. Allen
- Department of Chemistry, Boston University, Boston, MA 02215, USA
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38
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Higgins G, Higgins F, Peres J, Lang DM, Abdalrahman T, Zaman MH, Prince S, Franz T. Intracellular mechanics and TBX3 expression jointly dictate the spreading mode of melanoma cells in 3D environments. Exp Cell Res 2023; 428:113633. [PMID: 37172754 DOI: 10.1016/j.yexcr.2023.113633] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
Cell stiffness and T-box transcription factor 3 (TBX3) expression have been identified as biomarkers of melanoma metastasis in 2D environments. This study aimed to determine how mechanical and biochemical properties of melanoma cells change during cluster formation in 3D environments. Vertical growth phase (VGP) and metastatic (MET) melanoma cells were embedded in 3D collagen matrices of 2 and 4 mg/ml collagen concentrations, representing low and high matrix stiffness. Mitochondrial fluctuation, intracellular stiffness, and TBX3 expression were quantified before and during cluster formation. In isolated cells, mitochondrial fluctuation decreased and intracellular stiffness increased with increase in disease stage from VGP to MET and increased matrix stiffness. TBX3 was highly expressed in soft matrices but diminished in stiff matrices for VGP and MET cells. Cluster formation of VGP cells was excessive in soft matrices but limited in stiff matrices, whereas for MET cells it was limited in soft and stiff matrices. In soft matrices, VGP cells did not change the intracellular properties, whereas MET cells exhibited increased mitochondrial fluctuation and decreased TBX3 expression. In stiff matrices, mitochondrial fluctuation and TBX3 expression increased in VGP and MET, and intracellular stiffness increased in VGP but decreased in MET cells. The findings suggest that soft extracellular environments are more favourable for tumour growth, and high TBX3 levels mediate collective cell migration and tumour growth in the earlier VGP disease stage but play a lesser role in the later metastatic stage of melanoma.
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Affiliation(s)
- Ghodeejah Higgins
- Biomedical Engineering Research Centre, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Faatiemah Higgins
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Jade Peres
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Dirk M Lang
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Tamer Abdalrahman
- Biomedical Engineering Research Centre, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Muhammad H Zaman
- Department of Biomedical Engineering, Boston University, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sharon Prince
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Thomas Franz
- Biomedical Engineering Research Centre, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Observatory, South Africa; Bioengineering Science Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK.
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39
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Platania A, Erb C, Barbieri M, Molcrette B, Grandgirard E, de Kort MAC, Meaburn K, Taylor T, Shchuka VM, Kocanova S, Oliveira GM, Mitchell JA, Soutoglou E, Lenstra TL, Molina N, Papantonis A, Bystricky K, Sexton T. Competition between transcription and loop extrusion modulates promoter and enhancer dynamics. bioRxiv 2023:2023.04.25.538222. [PMID: 37162887 PMCID: PMC10168261 DOI: 10.1101/2023.04.25.538222] [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] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The spatiotemporal configuration of genes with distal regulatory elements, and the impact of chromatin mobility on transcription, remain unclear. Loop extrusion is an attractive model for bringing genetic elements together, but how this functionally interacts with transcription is also largely unknown. We combine live tracking of genomic loci and nascent transcripts with molecular dynamics simulations to assess the 4D arrangement of the Sox2 gene and its enhancer, in response to a battery of perturbations. We find that alterations in chromatin mobility, not promoter-enhancer distance, is more informative about transcriptional status. Active elements display more constrained mobility, consistent with confinement within specialized nuclear sites, and alterations in enhancer mobility distinguish poised from transcribing alleles. Strikingly, we find that whereas loop extrusion and transcription factor-mediated clustering contribute to promoter-enhancer proximity, they have antagonistic effects on chromatin dynamics. This provides an experimental framework for the underappreciated role of chromatin dynamics in genome regulation.
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Affiliation(s)
- Angeliki Platania
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Cathie Erb
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Mariano Barbieri
- Translational Epigenetics Group, Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Bastien Molcrette
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Erwan Grandgirard
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Marit AC de Kort
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Karen Meaburn
- Genome Damage and Stability Centre, Sussex University, School of Life Sciences, University of Sussex, Brighton, UK
| | - Tiegh Taylor
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Virlana M Shchuka
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Silvia Kocanova
- Molecular Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI) University of Toulouse Paul Sabatier, CNRS, 31062 Toulouse, France
| | - Guilherme Monteiro Oliveira
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Evi Soutoglou
- Genome Damage and Stability Centre, Sussex University, School of Life Sciences, University of Sussex, Brighton, UK
| | - Tineke L Lenstra
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Nacho Molina
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Argyris Papantonis
- Translational Epigenetics Group, Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Kerstin Bystricky
- Molecular Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI) University of Toulouse Paul Sabatier, CNRS, 31062 Toulouse, France
- Institut Universitaire de France (IUF)
| | - Tom Sexton
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
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40
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Huang J, Wu C, Kloeber JA, Gao H, Gao M, Zhu Q, Chang Y, Zhao F, Guo G, Luo K, Dai H, Liu S, Huang Q, Kim W, Zhou Q, Zhu S, Wu Z, Tu X, Yin P, Deng M, Wang L, Yuan J, Lou Z. SLFN5-mediated chromatin dynamics sculpt higher-order DNA repair topology. Mol Cell 2023; 83:1043-1060.e10. [PMID: 36854302 PMCID: PMC10467573 DOI: 10.1016/j.molcel.2023.02.004] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 12/23/2022] [Accepted: 02/01/2023] [Indexed: 03/02/2023]
Abstract
Repair of DNA double-strand breaks (DSBs) elicits three-dimensional (3D) chromatin topological changes. A recent finding reveals that 53BP1 assembles into a 3D chromatin topology pattern around DSBs. How this formation of a higher-order structure is configured and regulated remains enigmatic. Here, we report that SLFN5 is a critical factor for 53BP1 topological arrangement at DSBs. Using super-resolution imaging, we find that SLFN5 binds to 53BP1 chromatin domains to assemble a higher-order microdomain architecture by driving damaged chromatin dynamics at both DSBs and deprotected telomeres. Mechanistically, we propose that 53BP1 topology is shaped by two processes: (1) chromatin mobility driven by the SLFN5-LINC-microtubule axis and (2) the assembly of 53BP1 oligomers mediated by SLFN5. In mammals, SLFN5 deficiency disrupts the DSB repair topology and impairs non-homologous end joining, telomere fusions, class switch recombination, and sensitivity to poly (ADP-ribose) polymerase inhibitor. We establish a molecular mechanism that shapes higher-order chromatin topologies to safeguard genomic stability.
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Affiliation(s)
- Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Chenming Wu
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA; Medical Scientist Training Program, Mayo Clinic, Rochester, MN 55905, USA
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yiming Chang
- Jinzhou Medical University, Shanghai East Hospital, Shanghai 200120, China
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Haiming Dai
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Sijia Liu
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Qiru Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Wootae Kim
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Shouhai Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zheming Wu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xinyi Tu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Yuan
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200092, China.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA.
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41
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Goel S, Oliva R, Jeganathan S, Bader V, Krause LJ, Kriegler S, Stender ID, Christine CW, Nakamura K, Hoffmann JE, Winter R, Tatzelt J, Winklhofer KF. Linear ubiquitination induces NEMO phase separation to activate NF-κB signaling. Life Sci Alliance 2023; 6:e202201607. [PMID: 36720498 PMCID: PMC9889916 DOI: 10.26508/lsa.202201607] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 02/02/2023] Open
Abstract
The NF-κB essential modulator NEMO is the core regulatory component of the inhibitor of κB kinase complex, which is a critical checkpoint in canonical NF-κB signaling downstream of innate and adaptive immune receptors. In response to various stimuli, such as TNF or IL-1β, NEMO binds to linear or M1-linked ubiquitin chains generated by LUBAC, promoting its oligomerization and subsequent activation of the associated kinases. Here we show that M1-ubiquitin chains induce phase separation of NEMO and the formation of NEMO assemblies in cells after exposure to IL-1β. Phase separation is promoted by both binding of NEMO to linear ubiquitin chains and covalent linkage of M1-ubiquitin to NEMO and is essential but not sufficient for its phase separation. Supporting the functional relevance of NEMO phase separation in signaling, a pathogenic NEMO mutant, which is impaired in both binding and linkage to linear ubiquitin chains, does not undergo phase separation and is defective in mediating IL-1β-induced NF-κB activation.
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Affiliation(s)
- Simran Goel
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Rosario Oliva
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Sadasivam Jeganathan
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Laura J Krause
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Simon Kriegler
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Isabelle D Stender
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Ken Nakamura
- Department of Neurology, UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Jörg Tatzelt
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
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42
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Wittmann M, Voigtmann M, Simmchen J. Active BiVO 4 Swimmers Propelled by Depletion Gradients Caused by Photodeposition. Small 2023; 19:e2206885. [PMID: 36683219 DOI: 10.1002/smll.202206885] [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] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Artificial active matter often self-propels by creating gradients of one or more species or quantities. For chemical swimmers, most frequently either O2 or H+ that are created in certain catalytic reactions are causing the interfacial flows which drive the self-propulsion. While the palette of reactions is extending constantly, especially toward more bio-compatible fuels, the depletion of species is often overlooked. Here, the photodeposition of metal species on BiVO4 micro swimmers is considered. During the photodeposition reaction, metal ions are removed from the solution creating a depleted region around the particle. The ability of this depletion to drive active motion of artificial micro swimmers, as well as the influences of different metal ions and counter ions on the motion are investigated and cross compared.
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Affiliation(s)
- Martin Wittmann
- Chair of Physical Chemistry, TU Dresden, 01069, Dresden, Germany
| | | | - Juliane Simmchen
- Chair of Physical Chemistry, TU Dresden, 01069, Dresden, Germany
- Pure and applied Chemistry, University of Strathclyde, Glasgow, G1 1BX, UK
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43
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Puthukodan S, Hofmann M, Mairhofer M, Janout H, Schurr J, Hauser F, Naderer C, Preiner J, Winkler S, Sivun D, Jacak J. Purification Analysis, Intracellular Tracking, and Colocalization of Extracellular Vesicles Using Atomic Force and 3D Single-Molecule Localization Microscopy. Anal Chem 2023; 95:6061-6070. [PMID: 37002540 PMCID: PMC10100414 DOI: 10.1021/acs.analchem.3c00144] [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] [Indexed: 04/03/2023]
Abstract
Extracellular vesicles (EVs) play a key role in cell-cell communication and thus have great potential to be utilized as therapeutic agents and diagnostic tools. In this study, we implemented single-molecule microscopy techniques as a toolbox for a comprehensive characterization as well as measurement of the cellular uptake of HEK293T cell-derived EVs (eGFP-labeled) in HeLa cells. A combination of fluorescence and atomic force microscopy revealed a fraction of 68% fluorescently labeled EVs with an average size of ∼45 nm. Two-color single-molecule fluorescence microscopy analysis elucidated the 3D dynamics of EVs entering HeLa cells. 3D colocalization analysis of two-color direct stochastic optical reconstruction microscopy (dSTORM) images revealed that 25% of EVs that experienced uptake colocalized with transferrin, which has been linked to early recycling of endosomes and clathrin-mediated endocytosis. The localization analysis was combined with stepwise photobleaching, providing a comparison of protein aggregation outside and inside the cells.
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Affiliation(s)
| | - Martina Hofmann
- University of Applied Sciences Upper Austria, Linz 4020, Austria
| | - Mario Mairhofer
- University of Applied Sciences Upper Austria, Linz 4020, Austria
| | - Hannah Janout
- University of Applied Sciences Upper Austria, Hagenberg 4232, Austria
- Department of Computer Science, Johannes Kepler University, Linz 4040, Austria
| | - Jonas Schurr
- University of Applied Sciences Upper Austria, Hagenberg 4232, Austria
- Department of Computer Science, Johannes Kepler University, Linz 4040, Austria
| | - Fabian Hauser
- University of Applied Sciences Upper Austria, Linz 4020, Austria
| | | | - Johannes Preiner
- University of Applied Sciences Upper Austria, Linz 4020, Austria
| | - Stephan Winkler
- University of Applied Sciences Upper Austria, Hagenberg 4232, Austria
- Department of Computer Science, Johannes Kepler University, Linz 4040, Austria
| | - Dmitry Sivun
- University of Applied Sciences Upper Austria, Linz 4020, Austria
| | - Jaroslaw Jacak
- University of Applied Sciences Upper Austria, Linz 4020, Austria
- AUVA Research Center, Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Vienna 1200, Austria
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44
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Bai X, Sun P, Wang X, Long C, Liao S, Dang S, Zhuang S, Du Y, Zhang X, Li N, He K, Zhang Z. Structure and dynamics of the EGFR/HER2 heterodimer. Cell Discov 2023; 9:18. [PMID: 36781849 PMCID: PMC9925823 DOI: 10.1038/s41421-023-00523-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [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: 09/09/2022] [Accepted: 01/15/2023] [Indexed: 02/15/2023] Open
Abstract
HER2 belongs to the human epidermal growth factor receptor tyrosine kinase family. Its overexpression or hyperactivation is a leading cause for multiple types of cancers. HER2 functions mainly through dimerization with other family members, such as EGFR. However, the molecular details for heterodimer assembly have not been completely understood. Here, we report cryo-EM structures of the EGF- and epiregulin-bound EGFR/HER2 ectodomain complexes at resolutions of 3.3 Å and 4.5 Å, respectively. Together with the functional analyses, we demonstrate that only the dimerization arm of HER2, but not that of EGFR, is essential for their heterodimer formation and signal transduction. Moreover, we analyze the differential membrane dynamics and transient interactions of endogenous EGFR and HER2 molecules in genome-edited cells using single-molecule live-cell imaging. Furthermore, we show that the interaction with HER2 could allow EGFR to resist endocytosis. Together, this work deepens our understanding of the unique structural properties and dynamics of the EGFR/HER2 complex.
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Affiliation(s)
- Xue Bai
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
| | - Pengyu Sun
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Xinghao Wang
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Changkun Long
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
| | - Shuyun Liao
- grid.11135.370000 0001 2256 9319Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Song Dang
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shangshang Zhuang
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Yongtao Du
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Xinyi Zhang
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Nan Li
- grid.9227.e0000000119573309State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Kangmin He
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Zhe Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China. .,Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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45
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Fivenson EM, Rohs PD, Vettiger A, Sardis MF, Torres G, Forchoh A, Bernhardt TG. A role for the Gram-negative outer membrane in bacterial shape determination. bioRxiv 2023:2023.02.03.527047. [PMID: 36778245 PMCID: PMC9915748 DOI: 10.1101/2023.02.03.527047] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The cell envelope of Gram-negative bacteria consists of three distinct layers: the cytoplasmic membrane, a cell wall made of peptidoglycan (PG), and an asymmetric outer membrane (OM) composed of phospholipid in the inner leaflet and lipopolysaccharide (LPS) glycolipid in the outer leaflet. The PG layer has long been thought to be the major structural component of the envelope protecting cells from osmotic lysis and providing them with their characteristic shape. In recent years, the OM has also been shown to be a load-bearing layer of the cell surface that fortifies cells against internal turgor pressure. However, whether the OM also plays a role in morphogenesis has remained unclear. Here, we report that changes in LPS synthesis or modification predicted to strengthen the OM can suppress the growth and shape defects of Escherichia coli mutants with reduced activity in a conserved PG synthesis machine called the Rod system (elongasome) that is responsible for cell elongation and shape determination. Evidence is presented that OM fortification in the shape mutants restores the ability of MreB cytoskeletal filaments to properly orient the synthesis of new cell wall material by the Rod system. Our results are therefore consistent with a role for the OM in the propagation of rod shape during growth in addition to its well-known function as a diffusion barrier promoting the intrinsic antibiotic resistance of Gram-negative bacteria. SIGNIFICANCE The cell wall has traditionally been thought to be the main structural determinant of the bacterial cell envelope that resists internal turgor and determines cell shape. However, the outer membrane (OM) has recently been shown to contribute to the mechanical strength of Gram-negative bacterial envelopes. Here, we demonstrate that changes to OM composition predicted to increase its load bearing capacity rescue the growth and shape defects of Escherichia coli mutants defective in the major cell wall synthesis machinery that determines rod shape. Our results therefore reveal a previously unappreciated role for the OM in bacterial shape determination in addition to its well-known function as a diffusion barrier that protects Gram-negative bacteria from external insults like antibiotics.
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Affiliation(s)
- Elayne M. Fivenson
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Patricia D.A. Rohs
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Andrea Vettiger
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Marios F. Sardis
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Grasiela Torres
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Alison Forchoh
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Thomas G. Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
- Howard Hughes Medical Institute, Boston, United States
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46
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Bühler B, Schokolowski J, Benderoth A, Englert D, Grün F, Jäschke A, Sunbul M. Avidity-based bright and photostable light-up aptamers for single-molecule mRNA imaging. Nat Chem Biol 2023; 19:478-487. [PMID: 36658339 DOI: 10.1038/s41589-022-01228-8] [Citation(s) in RCA: 4] [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: 01/26/2022] [Accepted: 11/17/2022] [Indexed: 01/21/2023]
Abstract
Fluorescent light-up aptamers (FLAPs) have emerged as valuable tools to visualize RNAs, but are mostly limited by their poor brightness, low photostability, and high fluorescence background in live cells. Exploiting the avidity concept, here we present two of the brightest FLAPs with the strongest aptamer-dye interaction, high fluorogenicity, and remarkable photostability. They consist of dimeric fluorophore-binding aptamers (biRhoBAST and biSiRA) embedded in an RNA scaffold and their bivalent fluorophore ligands (bivalent tetramethylrhodamine TMR2 and silicon rhodamine SiR2). Red fluorescent biRhoBAST-TMR2 and near-infrared fluorescent biSiRA-SiR2 are orthogonal to each other, facilitating simultaneous visualization of two different RNA species in live cells. One copy of biRhoBAST allows for simple and robust mRNA imaging with strikingly higher signal-to-background ratios than other FLAPs. Moreover, eight biRhoBAST repeats enable single-molecule mRNA imaging and tracking with minimal perturbation of their localization, translation, and degradation, demonstrating the potential of avidity-enhanced FLAPs for imaging RNA dynamics.
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Affiliation(s)
- Bastian Bühler
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Janin Schokolowski
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Anja Benderoth
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Daniel Englert
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Franziska Grün
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
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47
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Tanimoto Y, Yoshimura Y, Hayashi F, Morigaki K. Retarded Diffusion and Confinement of Membrane-Bound Molecules in a Patterned Hybrid Membrane of Phospholipid Bilayers and Monolayers. J Phys Chem B 2023; 127:520-527. [PMID: 36598865 DOI: 10.1021/acs.jpcb.2c06053] [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] [Indexed: 01/05/2023]
Abstract
The biological membrane is a complex two-dimensional fluid, in which various molecular interactions regulate the lateral diffusion of membrane-associated molecules. Pinning of membrane proteins or lipids by extra-membrane proteins impedes the diffusion. In addition, coupling between two monolayer leaflets within a phospholipid bilayer via interdigitation plays important roles, though this effect remains elusive. Here, we fabricate a substrate-supported model membrane with patterned bilayer/monolayer regions to explore the influences of interleaflet coupling. A patterned monolayer of polymerized diacetylene phospholipid, 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine (DiynePC), was lithographically generated and used to form patterned lipid bilayers and monolayers. A phospholipid monolayer was formed on top of the polymerized monolayer. The bilayer/monolayer hybrid membrane was continuous and fluid, but lateral diffusion in the monolayer region was significantly retarded, suggesting the influences of interleaflet coupling. We reconstituted photoreceptor rhodopsin (Rh) and G-protein transducin (Gt) as model transmembrane and peripheral proteins. Rh diffused laterally only in the bilayer region, whereas Gt diffused in both bilayer and monolayer regions. The patterned hybrid bilayer/monolayer membrane reproduces the retarded diffusion and confinement of membrane-bound molecules in a controlled manner and provides insight into the physicochemical and functional roles of semipermeable corrals in the cell membrane.
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Affiliation(s)
- Yasushi Tanimoto
- Biosignal Research Center, Kobe University, Rokkodaicho 1-1, Nada, Kobe657-8501, Japan.,Graduate School of Science, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi, Osaka558-8585, Japan
| | - Yu Yoshimura
- Graduate School of Agricultural Science, Kobe University, Rokkodaicho 1-1, Nada, Kobe657-8501, Japan
| | - Fumio Hayashi
- Graduate School of Science, Kobe University, Rokkodaicho 1-1, Nada, Kobe657-8501, Japan
| | - Kenichi Morigaki
- Biosignal Research Center, Kobe University, Rokkodaicho 1-1, Nada, Kobe657-8501, Japan.,Graduate School of Agricultural Science, Kobe University, Rokkodaicho 1-1, Nada, Kobe657-8501, Japan
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48
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Suzuki T, De Nicola A, Okada T, Matsui H. Fully Atomistic Molecular Dynamics Simulation of a TIPS-Pentacene:Polystyrene Mixed Film Obtained via the Solution Process. Nanomaterials (Basel) 2023; 13:312. [PMID: 36678065 PMCID: PMC9860611 DOI: 10.3390/nano13020312] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/07/2023] [Accepted: 01/08/2023] [Indexed: 06/17/2023]
Abstract
Organic thin-film transistors using small-molecule semiconductor materials such as 6,13-bis(triisopropylsilylethynyl)pentacene (TIPS-P) have been recently studied for the production of flexible and printed electronic devices. Blending a semiconductor with an insulating polymer, such as polystyrene, is known to improve the device performance; however, its molecular-level structure remains unknown. In this study, we performed molecular dynamics (MD) simulations on a mixed system of TIPS-P and atactic polystyrene (aPS) with fully atomistic models to understand the structure of the mixed thin film at the molecular level and the influence on the device properties. To reproduce the deposition from the solution, we gradually reduced the number of toluene molecules in the simulation. The dynamic characteristics of the system, mean squared displacement, diffusion coefficient, density profile, and P2 order parameter were analyzed. Some of the simulated systems reached the equilibrium state. In these systems, the simulated structures suggested the presence of more TIPS-P molecules on the surface than inside the bulk, even at the low molecular weight of aPS, where phase separation was not observed experimentally. The results of the fully atomistic MD simulations are also a basis for the coarse-grained model to increase the speed of the MD simulation.
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Affiliation(s)
- Tomoka Suzuki
- Research Center for Organic Electronics (ROEL), Yamagata University, Jonan 4-3-16, Yonezawa 992-8510, Japan
| | - Antonio De Nicola
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Tomoharu Okada
- Research Center for Organic Electronics (ROEL), Yamagata University, Jonan 4-3-16, Yonezawa 992-8510, Japan
| | - Hiroyuki Matsui
- Research Center for Organic Electronics (ROEL), Yamagata University, Jonan 4-3-16, Yonezawa 992-8510, Japan
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Tas RP, Hendrix MMRM, Voets IK. Nanoscopy of single antifreeze proteins reveals that reversible ice binding is sufficient for ice recrystallization inhibition but not thermal hysteresis. Proc Natl Acad Sci U S A 2023; 120:e2212456120. [PMID: 36595705 DOI: 10.1073/pnas.2212456120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antifreeze proteins (AFPs) bind ice to reduce freezing temperatures and arrest ice crystal ripening, making AFPs essential for the survival of many organisms in ice-laden environments and attractive as biocompatible antifreezes in many applications. While their activity was identified over 50 years ago, the physical mechanisms through which they function are still debated because experimental insights at the molecular scale remain elusive. Here, we introduce subzero nanoscopy by the design and incorporation of a freezing stage on a commercial super-resolution setup to resolve the interfacial dynamics of single AFPs with ice crystal surfaces. Using this method, we demonstrate irreversible binding and immobilization (i.e., pinning) of individual proteins to the ice/water interface. Surprisingly, pinning is lost and adsorption becomes reversible when freezing point depression activity, but not ice recrystallization inhibition, is eliminated by a single mutation in the ice-binding site of the AFP. Our results provide direct experimental evidence for the adsorption-inhibition paradigm, pivotal to all theoretical descriptions of freezing point depression activity, but also reveal that reversible binding to ice must be accounted for in an all-inclusive model for AFP activity. These mechanistic insights into the relation between interfacial interactions and activity further our understanding and may serve as leading principles in the future design of highly potent, biocompatible antifreezes with tunable affinity.
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50
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Edwin PERG, Kumar S, Roy S, Roy B, Bajpai SK. Anisotropic 3D confinement of MCF-7 cells induces directed cell-migration and viscoelastic anisotropy of cell-membrane. Phys Biol 2023; 20. [DOI: 10.1088/1478-3975/ac9bc1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022]
Abstract
Abstract
Tumor-associated collagen signature-3 (TACS-3) is a prognostic indicator for breast cancer survival. It is characterized by highly organized, parallel bundles of collagen fibers oriented perpendicular to the tumor boundary, serving as directional, confining channels for cancer cell invasion. Here we design a TACS-3-mimetic anisotropic, confined collagen I matrix and examine the relation between anisotropy of matrix, directed cellular migration, and anisotropy of cell membrane-the first direct contact between TACS-3 and cell-using Michigan Cancer Foundation-7 (MCF-7) cells as cancer-model. Using unidirectional freezing, we generated ∼50 μm-wide channels filled with collagen I. Optical tweezer (OT) microrheology shows that anisotropic confinement increases collagen viscoelasticity by two orders of magnitude, and the elastic modulus is significantly greater along the direction of anisotropic confinement compared to that along the orthogonal direction, thus establishing matrix anisotropy. Furthermore, MCF-7 cells embedded in anisotropic collagen I, exhibit directionality in cellular morphology and migration. Finally, using customized OT to trap polystyrene probes bound to cell-membrane (and not to ECM) of either free cells or cells under anisotropic confinement, we quantified the effect of matrix anisotropy on membrane viscoelasticity, both in-plane and out-of-plane, vis-à-vis the membrane. Both bulk and viscous modulus of cell-membrane of MCF-7 cells exhibit significant anisotropy under anisotropic confinement. Moreover, the cell membrane of MCF-7 cells under anisotropic confinement is significantly softer (both in-plane and out-of-plane moduli) despite their local environment being five times stiffer than free cells. In order to test if the coupling between anisotropy of extracellular matrix and anisotropy of cell-membrane is regulated by cell-cytoskeleton, actin cytoskeleton was depolymerized for both free and confined cells. Results show that cell membrane viscoelasticity of confined MCF-7 cells is unaffected by actin de-polymerization, in contrast to free cells. Together, these findings suggest that anisotropy of ECM induces directed migration and correlates with anisotropy of cell-membrane viscoelasticity of the MCF-7 cells in an actin-independent manner.
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