1
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Solano A, Lou J, Scipioni L, Gratton E, Hinde E. Radial pair correlation of molecular brightness fluctuations maps protein diffusion as a function of oligomeric state within live-cell nuclear architecture. Biophys J 2022; 121:2152-2167. [PMID: 35490296 PMCID: PMC9247470 DOI: 10.1016/j.bpj.2022.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/16/2021] [Accepted: 04/26/2022] [Indexed: 11/22/2022] Open
Abstract
Nuclear proteins can modulate their DNA binding activity and the exploration volume available during DNA target search by self-associating into higher-order oligomers. Directly tracking this process in the nucleoplasm of a living cell is, however, a complex task. Thus, here we present a microscopy method based on radial pair correlation of molecular brightness fluctuations (radial pCOMB) that can extract the mobility of a fluorescently tagged nuclear protein as a function of its oligomeric state and spatiotemporally map the anisotropy of this parameter with respect to nuclear architecture. By simply performing a rapid frame scan acquisition, radial pCOMB has the capacity to detect, within each pixel, protein oligomer formation and the size-dependent obstruction nuclear architecture imparts on this complex's transport across sub-micrometer distances. From application of radial pCOMB to an oligomeric transcription factor and DNA repair protein, we demonstrate that homo-oligomer formation differentially regulates chromatin accessibility and interaction with the DNA template.
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Affiliation(s)
- Ashleigh Solano
- School of Physics, University of Melbourne; Department of Biochemistry and Pharmacology, University of Melbourne
| | - Jieqiong Lou
- School of Physics, University of Melbourne; Department of Biochemistry and Pharmacology, University of Melbourne
| | - Lorenzo Scipioni
- Department of Biomedical Engineering, University of California, Irvine
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine.
| | - Elizabeth Hinde
- School of Physics, University of Melbourne; Department of Biochemistry and Pharmacology, University of Melbourne.
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2
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Sallaberry I, Luszczak A, Philipp N, Navarro GSC, Gabriel MV, Gratton E, Gamarnik AV, Estrada LC. In vivo pair correlation microscopy reveals dengue virus capsid protein nucleocytoplasmic bidirectional movement in mammalian infected cells. Sci Rep 2021; 11:24415. [PMID: 34952906 PMCID: PMC8709865 DOI: 10.1038/s41598-021-03854-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/09/2021] [Indexed: 12/22/2022] Open
Abstract
Flaviviruses are major human disease-causing pathogens, including dengue virus (DENV), Zika virus, yellow fever virus and others. DENV infects hundreds of millions of people per year around the world, causing a tremendous social and economic burden. DENV capsid (C) protein plays an essential role during genome encapsidation and viral particle formation. It has been previously shown that DENV C enters the nucleus in infected cells. However, whether DENV C protein exhibits nuclear export remains unclear. By spatially cross-correlating different regions of the cell, we investigated DENV C movement across the nuclear envelope during the infection cycle. We observed that transport takes place in both directions and with similar translocation times (in the ms time scale) suggesting a bidirectional movement of both C protein import and export.Furthermore, from the pair cross-correlation functions in cytoplasmic or nuclear regions we found two populations of C molecules in each compartment with fast and slow mobilities. While in the cytoplasm the correlation times were in the 2-6 and 40-110 ms range for the fast and slow mobility populations respectively, in the cell nucleus they were 1-10 and 25-140 ms range, respectively. The fast mobility of DENV C in cytoplasmic and nuclear regions agreed with the diffusion coefficients from Brownian motion previously reported from correlation analysis. These studies provide the first evidence of DENV C shuttling from and to the nucleus in infected cells, opening new venues for antiviral interventions.
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Affiliation(s)
- Ignacio Sallaberry
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA-National Research Council for Science and Technology (CONICET), 1428, Buenos Aires, Argentina
| | - Alexis Luszczak
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA-National Research Council for Science and Technology (CONICET), 1428, Buenos Aires, Argentina
| | - Natalia Philipp
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA-National Research Council for Science and Technology (CONICET), 1428, Buenos Aires, Argentina
| | - Guadalupe S Costa Navarro
- Fundación Instituto Leloir-National Research Council for Science and Technology (CONICET), 1405, Buenos Aires, Argentina
| | - Manuela V Gabriel
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA-National Research Council for Science and Technology (CONICET), 1428, Buenos Aires, Argentina
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics and Beckman Laser Institute and Medical Clinic, University of California, Irvine, CA, USA
| | - Andrea V Gamarnik
- Fundación Instituto Leloir-National Research Council for Science and Technology (CONICET), 1405, Buenos Aires, Argentina
| | - Laura C Estrada
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA-National Research Council for Science and Technology (CONICET), 1428, Buenos Aires, Argentina.
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3
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McCann AJ, Lou J, Moustaqil M, Graus MS, Blum A, Fontaine F, Liu H, Luu W, Rudolffi-Soto P, Koopman P, Sierecki E, Gambin Y, Meunier FA, Liu Z, Hinde E, Francois M. A dominant-negative SOX18 mutant disrupts multiple regulatory layers essential to transcription factor activity. Nucleic Acids Res 2021; 49:10931-10955. [PMID: 34570228 PMCID: PMC8565327 DOI: 10.1093/nar/gkab820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 08/18/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022] Open
Abstract
Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism underlying a dominant-negative form of the SOX18 transcription factor (SOX18RaOp) responsible for both the classical mouse mutant Ragged Opossum and the human genetic disorder Hypotrichosis-lymphedema-telangiectasia-renal defect syndrome. Combining three single-molecule imaging assays in living cells together with genomics and proteomics analysis, we found that SOX18RaOp disrupts the system through an accumulation of molecular interferences which impair several functional properties of the wild-type SOX18 protein, including its target gene selection process. The dominant-negative effect is further amplified by poisoning the interactome of its wild-type counterpart, which perturbs regulatory nodes such as SOX7 and MEF2C. Our findings explain in unprecedented detail the multi-layered process that underpins the molecular aetiology of dominant-negative transcription factor function.
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Affiliation(s)
- Alex J McCann
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jieqiong Lou
- School of Physics, Department of Biochemistry and Molecular Biology, Bio21, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mehdi Moustaqil
- EMBL Australia Node in Single Molecule Science and School of Medical Sciences, The University of New South Wales, Sydney, NSW 1466, Australia
| | - Matthew S Graus
- The David Richmond Laboratory for Cardio-Vascular Development: gene regulation and editing, The Centenary Institute, Newtown, Sydney, NSW 2006, Australia
| | - Ailisa Blum
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Frank Fontaine
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Hui Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, United States
| | - Winnie Luu
- The David Richmond Laboratory for Cardio-Vascular Development: gene regulation and editing, The Centenary Institute, Newtown, Sydney, NSW 2006, Australia
| | - Paulina Rudolffi-Soto
- EMBL Australia Node in Single Molecule Science and School of Medical Sciences, The University of New South Wales, Sydney, NSW 1466, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Science and School of Medical Sciences, The University of New South Wales, Sydney, NSW 1466, Australia
| | - Yann Gambin
- EMBL Australia Node in Single Molecule Science and School of Medical Sciences, The University of New South Wales, Sydney, NSW 1466, Australia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, United States
| | - Elizabeth Hinde
- School of Physics, Department of Biochemistry and Molecular Biology, Bio21, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mathias Francois
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.,The David Richmond Laboratory for Cardio-Vascular Development: gene regulation and editing, The Centenary Institute, Newtown, Sydney, NSW 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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4
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Zentout S, Smith R, Jacquier M, Huet S. New Methodologies to Study DNA Repair Processes in Space and Time Within Living Cells. Front Cell Dev Biol 2021; 9:730998. [PMID: 34589495 PMCID: PMC8473836 DOI: 10.3389/fcell.2021.730998] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/25/2021] [Indexed: 01/02/2023] Open
Abstract
DNA repair requires a coordinated effort from an array of factors that play different roles in the DNA damage response from recognizing and signaling the presence of a break, creating a repair competent environment, and physically repairing the lesion. Due to the rapid nature of many of these events, live-cell microscopy has become an invaluable method to study this process. In this review we outline commonly used tools to induce DNA damage under the microscope and discuss spatio-temporal analysis tools that can bring added information regarding protein dynamics at sites of damage. In particular, we show how to go beyond the classical analysis of protein recruitment curves to be able to assess the dynamic association of the repair factors with the DNA lesions as well as the target-search strategies used to efficiently find these lesions. Finally, we discuss how the use of mathematical models, combined with experimental evidence, can be used to better interpret the complex dynamics of repair proteins at DNA lesions.
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Affiliation(s)
- Siham Zentout
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, Rennes, France
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, Rennes, France
| | - Marine Jacquier
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, Rennes, France
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, Rennes, France
- Institut Universitaire de France, Paris, France
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5
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Pinto-Cámara R, Linares A, Moreno-Gutiérrez DS, Hernández HO, Martínez-Reyes JD, Rendón-Mancha JM, Wood CD, Guerrero A. FCSlib: an open-source tool for fluorescence fluctuation spectroscopy analysis for mobility, number and molecular brightness in R. Bioinformatics 2021; 37:1930-1931. [PMID: 33051645 DOI: 10.1093/bioinformatics/btaa876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/01/2020] [Accepted: 09/28/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY FCSlib is an open-source R tool for fluorescence fluctuation spectroscopy data analysis. It encompasses techniques such as Fluorescence Correlation Spectroscopy, Number and Brightness, Pair Correlation Function and Pair Correlation of Molecular Brightness. AVAILABILITY AND IMPLEMENTATION Source code available at https://cran.r-project.org/web/packages/FCSlib/ for Linux, Windows and macOS platforms. Sample data as well as a user's guide are available at https://github.com/FCSlib/FCSlib. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- R Pinto-Cámara
- Departamento de Genética del Desarrollo y Fisiología Molecular, Laboratorio Nacional de Microscopía Avanzada
| | - A Linares
- Departamento de Genética del Desarrollo y Fisiología Molecular, Laboratorio Nacional de Microscopía Avanzada
| | - D S Moreno-Gutiérrez
- Departamento de Computación y Robótica, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Morelos, México
| | - H O Hernández
- Departamento de Ciencias de la Computación, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - J D Martínez-Reyes
- Departamento de Genética del Desarrollo y Fisiología Molecular, Laboratorio Nacional de Microscopía Avanzada
| | - J M Rendón-Mancha
- Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, 62209 Cuernavaca, Morelos, México
| | - C D Wood
- Departamento de Genética del Desarrollo y Fisiología Molecular, Laboratorio Nacional de Microscopía Avanzada
| | - A Guerrero
- Departamento de Genética del Desarrollo y Fisiología Molecular, Laboratorio Nacional de Microscopía Avanzada
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6
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Diallo M, Herrera F. The role of understudied post-translational modifications for the behavior and function of Signal Transducer and Activator of Transcription 3. FEBS J 2021; 289:6235-6255. [PMID: 34235865 DOI: 10.1111/febs.16116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/16/2021] [Accepted: 07/07/2021] [Indexed: 12/19/2022]
Abstract
The Signal Transducer and Activator of Transcription (STAT) family of transcription factors is involved in inflammation, immunity, development, cancer, and response to injury, among other biological phenomena. Canonical STAT signaling is often represented as a 3-step pathway involving the sequential activation of a membrane receptor, an intermediate kinase, and a STAT transcription factor. The rate-limiting phosphorylation at a highly conserved C-terminal tyrosine residue determines the nuclear translocation and transcriptional activity of STATs. This apparent simplicity is actually misleading and can hardly explain the pleiotropic nature of STATs, the existence of various noncanonical STAT pathways, or the key role of the N-terminal domain in STAT functions. More than 80 post-translational modifications (PTMs) have been identified for STAT3, but their functions remain barely understood. Here, we provide a brief but comprehensive overview of these underexplored PTMs and their role on STAT3 canonical and noncanonical functions. A less tyrosine-centric point of view may be required to advance our understanding of STAT signaling.
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Affiliation(s)
- Mickael Diallo
- Faculdade de Ciências da Universidade de Lisboa, Cell Structure and Dynamics Laboratory, BioISI - Instituto de Biosistemas e Ciências integrativas, Lisbon, Portugal.,MOSTMICRO Research Unit, Instituto de Tecnologia Química e Biológica (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Federico Herrera
- Faculdade de Ciências da Universidade de Lisboa, Cell Structure and Dynamics Laboratory, BioISI - Instituto de Biosistemas e Ciências integrativas, Lisbon, Portugal.,MOSTMICRO Research Unit, Instituto de Tecnologia Química e Biológica (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
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7
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Eberherr AC, Maaske A, Wolf C, Giesert F, Berutti R, Rusha E, Pertek A, Kastlmeier MT, Voss C, Plummer M, Sayed A, Graf E, Effner R, Volz T, Drukker M, Strom TM, Meitinger T, Stoeger T, Buyx AM, Hagl B, Renner ED. Rescue of STAT3 Function in Hyper-IgE Syndrome Using Adenine Base Editing. CRISPR J 2021; 4:178-190. [PMID: 33876960 DOI: 10.1089/crispr.2020.0111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
STAT3-hyper IgE syndrome (STAT3-HIES) is a primary immunodeficiency presenting with destructive lung disease along with other symptoms. CRISPR-Cas9-mediated adenine base editors (ABEs) have the potential to correct one of the most common STAT3-HIES causing heterozygous STAT3 mutations (c.1144C>T/p.R382W). As a proof-of-concept, we successfully applied ABEs to correct STAT3 p.R382W in patient fibroblasts and induced pluripotent stem cells (iPSCs). Treated primary STAT3-HIES patient fibroblasts showed a correction efficiency of 29% ± 7% without detectable off-target effects evaluated through whole-genome and high-throughput sequencing. Compared with untreated patient fibroblasts, corrected single-cell clones showed functional rescue of STAT3 signaling with significantly increased STAT3 DNA-binding activity and target gene expression of CCL2 and SOCS3. Patient-derived iPSCs were corrected with an efficiency of 30% ± 6% and differentiated to alveolar organoids showing preserved plasticity in treated cells. In conclusion, our results are supportive for ABE-based gene correction as a potential causative treatment of STAT3-HIES.
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Affiliation(s)
- Andreas C Eberherr
- Translational Immunology in Environmental Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany; Technical University of Munich, Munich, Germany.,Translational Immunology, Institute of Environmental Medicine, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Andre Maaske
- Translational Immunology in Environmental Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany; Technical University of Munich, Munich, Germany.,Translational Immunology, Institute of Environmental Medicine, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Christine Wolf
- Translational Immunology in Environmental Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany; Technical University of Munich, Munich, Germany.,Translational Immunology, Institute of Environmental Medicine, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany.,Chair of Developmental Genetics, Technical University of Munich, Munich, Germany; Technical University of Munich, Munich, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, Technical University of Munich, Munich, Germany; Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Ejona Rusha
- iPSC Core Facility, Institute of Stem Cell Research, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Anna Pertek
- iPSC Core Facility, Institute of Stem Cell Research, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Miriam T Kastlmeier
- Institute of Lung Biology and Disease, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Carola Voss
- Institute of Lung Biology and Disease, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Michelle Plummer
- Translational Immunology in Environmental Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany; Technical University of Munich, Munich, Germany.,Translational Immunology, Institute of Environmental Medicine, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Amina Sayed
- Translational Immunology in Environmental Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany; Technical University of Munich, Munich, Germany.,Translational Immunology, Institute of Environmental Medicine, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany.,Institute of Lung Biology and Disease, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Renate Effner
- Translational Immunology in Environmental Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany; Technical University of Munich, Munich, Germany.,Translational Immunology, Institute of Environmental Medicine, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Thomas Volz
- Department of Dermatology and Allergology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany; and Technical University of Munich, Munich, Germany
| | - Micha Drukker
- iPSC Core Facility, Institute of Stem Cell Research, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Tim M Strom
- Institute of Human Genetics, Technical University of Munich, Munich, Germany; Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technical University of Munich, Munich, Germany; Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Tobias Stoeger
- Institute of Lung Biology and Disease, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Alena M Buyx
- Institute for History and Ethics of Medicine, Technical University of Munich, Munich, Germany
| | - Beate Hagl
- Translational Immunology in Environmental Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany; Technical University of Munich, Munich, Germany.,Translational Immunology, Institute of Environmental Medicine, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
| | - Ellen D Renner
- Translational Immunology in Environmental Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany; Technical University of Munich, Munich, Germany.,Translational Immunology, Institute of Environmental Medicine, Helmholtz Zentrum Munich, Neuherberg, Germany; Technical University of Munich, Munich, Germany
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8
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Işbilir A, Serfling R, Möller J, Thomas R, De Faveri C, Zabel U, Scarselli M, Beck-Sickinger AG, Bock A, Coin I, Lohse MJ, Annibale P. Determination of G-protein-coupled receptor oligomerization by molecular brightness analyses in single cells. Nat Protoc 2021; 16:1419-1451. [PMID: 33514946 DOI: 10.1038/s41596-020-00458-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/03/2020] [Indexed: 02/08/2023]
Abstract
Oligomerization of membrane proteins has received intense research interest because of their importance in cellular signaling and the large pharmacological and clinical potential this offers. Fluorescence imaging methods are emerging as a valid tool to quantify membrane protein oligomerization at high spatial and temporal resolution. Here, we provide a detailed protocol for an image-based method to determine the number and oligomerization state of fluorescently labeled prototypical G-protein-coupled receptors (GPCRs) on the basis of small out-of-equilibrium fluctuations in fluorescence (i.e., molecular brightness) in single cells. The protocol provides a step-by-step procedure that includes instructions for (i) a flexible labeling strategy for the protein of interest (using fluorescent proteins, small self-labeling tags or bio-orthogonal labeling) and the appropriate controls, (ii) performing temporal and spatial brightness image acquisition on a confocal microscope and (iii) analyzing and interpreting the data, excluding clusters and intensity hot-spots commonly observed in receptor distributions. Although specifically tailored for GPCRs, this protocol can be applied to diverse classes of membrane proteins of interest. The complete protocol can be implemented in 1 month.
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Affiliation(s)
- Ali Işbilir
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Robert Serfling
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Jan Möller
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Romy Thomas
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Chiara De Faveri
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Ulrike Zabel
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Marco Scarselli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Andreas Bock
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Martin J Lohse
- Max Delbrück Center for Molecular Medicine, Berlin, Germany. .,Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany. .,ISAR Bioscience Institute, Munich, Germany.
| | - Paolo Annibale
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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9
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Lou J, Priest DG, Solano A, Kerjouan A, Hinde E. Spatiotemporal dynamics of 53BP1 dimer recruitment to a DNA double strand break. Nat Commun 2020; 11:5776. [PMID: 33188174 PMCID: PMC7666136 DOI: 10.1038/s41467-020-19504-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 10/15/2020] [Indexed: 01/08/2023] Open
Abstract
Tumor suppressor p53-binding protein 1 (53BP1) is a DNA repair protein essential for the detection, assessment, and resolution of DNA double strand breaks (DSBs). The presence of a DSB is signaled to 53BP1 via a local histone modification cascade that triggers the binding of 53BP1 dimers to chromatin flanking this type of lesion. While biochemical studies have established that 53BP1 exists as a dimer, it has never been shown in a living cell when or where 53BP1 dimerizes upon recruitment to a DSB site, or upon arrival at this nuclear location, how the DSB histone code to which 53BP1 dimers bind regulates retention and self-association into higher-order oligomers. Thus, here in live-cell nuclear architecture we quantify the spatiotemporal dynamics of 53BP1 oligomerization during a DSB DNA damage response by coupling fluorescence fluctuation spectroscopy (FFS) with the DSB inducible via AsiSI cell system (DIvA). From adopting this multiplexed approach, we find that preformed 53BP1 dimers relocate from the nucleoplasm to DSB sites, where consecutive recognition of ubiquitinated lysine 15 of histone 2A (H2AK15ub) and di-methylated lysine 20 of histone 4 (H4K20me2), leads to the assembly of 53BP1 oligomers and a mature 53BP1 foci structure.
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Affiliation(s)
- Jieqiong Lou
- School of Physics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - David G Priest
- School of Physics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Ashleigh Solano
- School of Physics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Adèle Kerjouan
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Elizabeth Hinde
- School of Physics, University of Melbourne, Melbourne, Victoria, Australia. .,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.
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10
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Li B, Xie S, Xia A, Suo T, Huang H, Zhang X, Chen Y, Zhou X. Recent advance in the sensing of biomarker transcription factors. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116039] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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11
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La Sala G, Michiels C, Kükenshöner T, Brandstoetter T, Maurer B, Koide A, Lau K, Pojer F, Koide S, Sexl V, Dumoutier L, Hantschel O. Selective inhibition of STAT3 signaling using monobodies targeting the coiled-coil and N-terminal domains. Nat Commun 2020; 11:4115. [PMID: 32807795 PMCID: PMC7431413 DOI: 10.1038/s41467-020-17920-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 07/27/2020] [Indexed: 12/23/2022] Open
Abstract
The transcription factor STAT3 is frequently activated in human solid and hematological malignancies and remains a challenging therapeutic target with no approved drugs to date. Here, we develop synthetic antibody mimetics, termed monobodies, to interfere with STAT3 signaling. These monobodies are highly selective for STAT3 and bind with nanomolar affinity to the N-terminal and coiled-coil domains. Interactome analysis detects no significant binding to other STATs or additional off-target proteins, confirming their exquisite specificity. Intracellular expression of monobodies fused to VHL, an E3 ubiquitin ligase substrate receptor, results in degradation of endogenous STAT3. The crystal structure of STAT3 in complex with monobody MS3-6 reveals bending of the coiled-coil domain, resulting in diminished DNA binding and nuclear translocation. MS3-6 expression strongly inhibits STAT3-dependent transcriptional activation and disrupts STAT3 interaction with the IL-22 receptor. Therefore, our study establishes innovative tools to interfere with STAT3 signaling by different molecular mechanisms. STAT3 is an attractive therapeutic target but its homology with other STAT proteins complicates the development of selective inhibitors. Here, the authors develop monobodies with high affinity and selectivity for STAT3 and show that they can interfere with cellular STAT3 activity.
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Affiliation(s)
- Grégory La Sala
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Camille Michiels
- Experimental Medicine Unit, De Duve Institute, Université catholique de Louvain, 1200, Brussels, Belgium
| | - Tim Kükenshöner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Tania Brandstoetter
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Barbara Maurer
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Akiko Koide
- Department of Medicine, New York University School of Medicine, 522 1st Avenue, New York, 10016, NY, USA.,Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, 522 1st Avenue, New York, 10016, NY, USA
| | - Kelvin Lau
- Protein Crystallography Core Facility, School of Life Sciences, École polytechnique fédérale de Lausanne, Station 19, 1015, Lausanne, Switzerland
| | - Florence Pojer
- Protein Crystallography Core Facility, School of Life Sciences, École polytechnique fédérale de Lausanne, Station 19, 1015, Lausanne, Switzerland
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, 522 1st Avenue, New York, 10016, NY, USA.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 1st Avenue, New York, 10016, NY, USA
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | - Laure Dumoutier
- Experimental Medicine Unit, De Duve Institute, Université catholique de Louvain, 1200, Brussels, Belgium
| | - Oliver Hantschel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland. .,Faculty of Medicine, Institute of Physiological Chemistry, Philipps-University of Marburg, Karl-von-Frisch-Straße 1, 35032, Marburg, Germany.
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12
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Petazzi RA, Aji AK, Chiantia S. Fluorescence microscopy methods for the study of protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:1-41. [DOI: 10.1016/bs.pmbts.2019.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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13
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Paakinaho V, Johnson TA, Presman DM, Hager GL. Glucocorticoid receptor quaternary structure drives chromatin occupancy and transcriptional outcome. Genome Res 2019; 29:1223-1234. [PMID: 31337711 PMCID: PMC6673716 DOI: 10.1101/gr.244814.118] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 04/09/2019] [Indexed: 01/11/2023]
Abstract
Most transcription factors, including nuclear receptors, are widely modeled as binding regulatory elements as monomers, homodimers, or heterodimers. Recent findings in live cells show that the glucocorticoid receptor NR3C1 (also known as GR) forms tetramers on enhancers, owing to an allosteric alteration induced by DNA binding, and suggest that higher oligomerization states are important for the gene regulatory responses of GR. By using a variant (GRtetra) that mimics this allosteric transition, we performed genome-wide studies using a GR knockout cell line with reintroduced wild-type GR or reintroduced GRtetra. GRtetra acts as a super receptor by binding to response elements not accessible to the wild-type receptor and both induces and represses more genes than GRwt. These results argue that DNA binding induces a structural transition to the tetrameric state, forming a transient higher-order structure that drives both the activating and repressive actions of glucocorticoids.
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Affiliation(s)
- Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA.,Institute of Biomedicine, University of Eastern Finland, Kuopio, FI-70211 Kuopio, Finland
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA.,IFIBYNE, UBA-CONICET, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, C1428EGA, Argentina
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA
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14
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Fluorescence fluctuation spectroscopy: an invaluable microscopy tool for uncovering the biophysical rules for navigating the nuclear landscape. Biochem Soc Trans 2019; 47:1117-1129. [DOI: 10.1042/bst20180604] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Nuclear architecture is fundamental to the manner by which molecules traverse the nucleus. The nucleoplasm is a crowded environment where dynamic rearrangements in local chromatin compaction locally redefine the space accessible toward nuclear protein diffusion. Here, we review a suite of methods based on fluorescence fluctuation spectroscopy (FFS) and how they have been employed to interrogate chromatin organization, as well as the impact this structural framework has on nuclear protein target search. From first focusing on a set of studies that apply FFS to an inert fluorescent tracer diffusing inside the nucleus of a living cell, we demonstrate the capacity of this technology to measure the accessibility of the nucleoplasm. Then with a baseline understanding of the exploration volume available to nuclear proteins during target search, we review direct applications of FFS to fluorescently labeled transcription factors (TFs). FFS can detect changes in TF mobility due to DNA binding, as well as the formation of TF complexes via changes in brightness due to oligomerization. Collectively, we find that FFS-based methods can uncover how nuclear proteins in general navigate the nuclear landscape.
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15
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Royer CA. Characterizing proteins in their cellular environment: Examples of recent advances in quantitative fluorescence microscopy. Protein Sci 2019; 28:1210-1221. [PMID: 31012169 DOI: 10.1002/pro.3630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/20/2019] [Accepted: 04/22/2019] [Indexed: 11/12/2022]
Abstract
Quantitative characterization of protein interactions, both intramolecular and intermolecular, is crucial in understanding the mechanisms and regulation of their function. In recent years, it has become possible to obtain such information on protein systems in live cells, from bacteria to mammalian cell lines. This review discusses recent advances in measuring protein folding, absolute concentration, oligomerization, diffusion, transport, and organization at super-resolution.
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Affiliation(s)
- Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180
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16
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Cutrale F, Rodriguez D, Hortigüela V, Chiu CL, Otterstrom J, Mieruszynski S, Seriola A, Larrañaga E, Raya A, Lakadamyali M, Fraser SE, Martinez E, Ojosnegros S. Using enhanced number and brightness to measure protein oligomerization dynamics in live cells. Nat Protoc 2019; 14:616-638. [DOI: 10.1038/s41596-018-0111-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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17
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Ponatinib Inhibits Multiple Signaling Pathways Involved in STAT3 Signaling and Attenuates Colorectal Tumor Growth. Cancers (Basel) 2018; 10:cancers10120526. [PMID: 30572654 PMCID: PMC6316865 DOI: 10.3390/cancers10120526] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022] Open
Abstract
Signal transducer and activator of transcription 3 (STAT3) signaling is a major driver of colorectal cancer (CRC) growth, however therapeutics, which can effectively target this pathway, have so far remained elusive. Here, we performed an extensive screen for STAT3 inhibitors among a library of 1167 FDA-approved agents, identifying Ponatinib as a lead candidate. We found that Ponatinib inhibits STAT3 activity driven by EGF/EGFR, IL-6/IL-6R and IL-11/IL-11R, three major ligand/receptor systems involved in CRC development and progression. Ponatinib was able to inhibit CRC migration and tumor growth in vivo. In addition, Ponatinib displayed a greater ability to inhibit STAT3 activity and mediated superior anti-proliferative efficacy compared to five FDA approved SRC and Janus Kinase (JAK) inhibitors. Finally, long-term exposure of CRC cells to Ponatinib, Dasatinib and Bosutinib resulted in acquired resistance to Dasatinib and Bosutinib occurring within six weeks. However, acquired resistance to Ponatinib was observed after long-term exposure of >4 months. Overall, our results identify a novel anti-STAT3 property of Ponatinib and thus, Ponatinib offers a potential therapeutic strategy for CRC.
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18
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Yong X, Yang X, Emory SR, Wang J, Dai J, Yu X, Mei L, Xie J, Ruan G. A potent, minimally invasive and simple strategy of enhancing intracellular targeted delivery of Tat peptide-conjugated quantum dots: organic solvent-based permeation enhancer. Biomater Sci 2018; 6:3085-3095. [PMID: 30303500 DOI: 10.1039/c8bm00928g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Targeted delivery of nanomaterials to specific intracellular locations is essential for the development of many nanomaterials-based biological applications. Thus far the targeting performance has been limited due to various intracellular transport barriers, especially intracellular vesicle trapping. Here we report the application of permeation enhancers based on organic solvents in small percentage to enhance the intracellular targeted delivery of nanomaterials. Previously permeation enhancers based on organic solvents and ionic liquids have been used in overcoming biological transport barriers at tissue, organ, and cellular levels, but this strategy has so far rarely been examined for its potential in facilitating transport of nanometer-scale entities across intracellular barriers, particularly intracellular vesicle trapping. Using the cell nucleus as a model intracellular target and Tat peptide-conjugated quantum dots (QDs-Tat) as a model nanomaterial-based probe, we demonstrate that a small percentage (e.g. 1%) of organic solvent greatly enhances nucleus targeting specificity as well as increasing endocytosis-based cellular uptake of QDs. We combine vesicle colocalization (DiO dye staining), vesicle integrity (calcein dye release), and single-particle studies (pair-correlation function microscopy) to investigate the process of organic solvent-enhanced vesicle escape of QDs-Tat. The organic solvent based vesicle escape-enhancing approach is found to be not only very effective but minimally invasive, resulting in high vesicle escape efficiency with no significant disruption to the membrane integrity of either intracellular vesicles or cells. This approach drastically outperforms the commonly used vesicle escape-enhancing agent (i.e., chloroquine, whose enhancement effect is based on disrupting vesicle integrity) in both potency and minimal invasiveness. Finally, we apply organic solvent-based targeting enhancement to improve the intracellular delivery of the anticancer drug doxorubicin (DOX).
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Affiliation(s)
- Xueqing Yong
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, China. and Institute of Materials Engineering, College of Engineering and Applied Sciences, Nanjing University, China and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, China
| | - Xuan Yang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, China. and Institute of Materials Engineering, College of Engineering and Applied Sciences, Nanjing University, China and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, China
| | - Steven R Emory
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, China. and Institute of Materials Engineering, College of Engineering and Applied Sciences, Nanjing University, China and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, China and Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Jun Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, China. and Institute of Materials Engineering, College of Engineering and Applied Sciences, Nanjing University, China and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, China
| | - Jie Dai
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, China. and Institute of Materials Engineering, College of Engineering and Applied Sciences, Nanjing University, China and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, China
| | - Xiaoya Yu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, China. and Institute of Materials Engineering, College of Engineering and Applied Sciences, Nanjing University, China and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, China
| | - Ling Mei
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, China. and Institute of Materials Engineering, College of Engineering and Applied Sciences, Nanjing University, China and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, China
| | - Jinbing Xie
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, China. and Institute of Materials Engineering, College of Engineering and Applied Sciences, Nanjing University, China and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, China
| | - Gang Ruan
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, China. and Institute of Materials Engineering, College of Engineering and Applied Sciences, Nanjing University, China and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, China
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19
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Arora L, Kumar AP, Arfuso F, Chng WJ, Sethi G. The Role of Signal Transducer and Activator of Transcription 3 (STAT3) and Its Targeted Inhibition in Hematological Malignancies. Cancers (Basel) 2018; 10:cancers10090327. [PMID: 30217007 PMCID: PMC6162647 DOI: 10.3390/cancers10090327] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 12/22/2022] Open
Abstract
Signal transducer and activator of transcription 3 (STAT3), a member of the STAT protein family, can be phosphorylated by receptor-associated Janus kinases (JAKs) in response to stimulation by cytokines and growth factors. It forms homo- or heterodimers that can translocate to the cell nucleus where they act as transcription activators. Constitutive activation of STAT3 has been found to be associated with initiation and progression of various cancers. It can exert proliferative as well as anti-apoptotic effects. This review focuses on the role of STAT3 in pathogenesis i.e., proliferation, differentiation, migration, and apoptosis of hematological malignancies viz. leukemia, lymphoma and myeloma, and briefly highlights the potential therapeutic approaches developed against STAT3 activation pathway.
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Affiliation(s)
- Loukik Arora
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore.
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore.
- Cancer Science Institute of Singapore, Centre for Translational Medicine, 14 Medical Drive, #11-01M, Singapore 117599, Singapore.
- Medical Science Cluster, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore.
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Perth, WA 6102, Australia.
- National University Cancer Institute, National University Health System, Singapore 119074, Singapore.
| | - Frank Arfuso
- Stem Cell and Cancer Biology Laboratory, School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia.
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, Centre for Translational Medicine, 14 Medical Drive, #11-01M, Singapore 117599, Singapore.
- Department of Hematology-Oncology, National University Cancer Institute, National University Health System, Singapore 119074, Singapore.
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore.
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6009, Australia.
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20
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Papini C, Royer CA. Scanning number and brightness yields absolute protein concentrations in live cells: a crucial parameter controlling functional bio-molecular interaction networks. Biophys Rev 2018; 10:87-96. [PMID: 29383593 DOI: 10.1007/s12551-017-0394-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/29/2017] [Indexed: 12/27/2022] Open
Abstract
Biological function results from properly timed bio-molecular interactions that transduce external or internal signals, resulting in any number of cellular fates, including triggering of cell-state transitions (division, differentiation, transformation, apoptosis), metabolic homeostasis and adjustment to changing physical or nutritional environments, amongst many more. These bio-molecular interactions can be modulated by chemical modifications of proteins, nucleic acids, lipids and other small molecules. They can result in bio-molecular transport from one cellular compartment to the other and often trigger specific enzyme activities involved in bio-molecular synthesis, modification or degradation. Clearly, a mechanistic understanding of any given high level biological function requires a quantitative characterization of the principal bio-molecular interactions involved and how these may change dynamically. Such information can be obtained using fluctation analysis, in particular scanning number and brightness, and used to build and test mechanistic models of the functional network to define which characteristics are the most important for its regulation.
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Affiliation(s)
- Christina Papini
- Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Catherine A Royer
- Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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21
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Nolan R, Iliopoulou M, Alvarez L, Padilla-Parra S. Detecting protein aggregation and interaction in live cells: A guide to number and brightness. Methods 2017; 140-141:172-177. [PMID: 29221925 DOI: 10.1016/j.ymeth.2017.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/01/2017] [Accepted: 12/03/2017] [Indexed: 12/31/2022] Open
Abstract
The possibility to detect and quantify protein-protein interactions with good spatial and temporal resolutions in live cells is crucial in biology. Number and brightness is a powerful approach to detect both protein aggregation/desegregation dynamics and stoichiometry in live cells. Importantly, this technique can be applied in commercial set ups: both camera based and laser scanning microscopes. It provides pixel-by-pixel information on protein oligomeric states. If performed with two colours, the technique can retrieve the stoichiometry of the reaction under study. In this review, we discuss the strengths and weaknesses of the technique, stressing which are the correct acquisition parameters for a given microscope, the main challenges in analysis, and the limitations of the technique.
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Affiliation(s)
- Rory Nolan
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Maro Iliopoulou
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Luis Alvarez
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Sergi Padilla-Parra
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK.
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22
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Cardarelli F. Time-resolved biophysical approaches to nucleocytoplasmic transport. Comput Struct Biotechnol J 2017; 15:299-306. [PMID: 28435614 PMCID: PMC5388937 DOI: 10.1016/j.csbj.2017.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/21/2017] [Accepted: 03/25/2017] [Indexed: 12/26/2022] Open
Abstract
Molecules are continuously shuttling across the nuclear envelope barrier that separates the nucleus from the cytoplasm. Instead of being just a barrier to diffusion, the nuclear envelope is rather a complex filter that provides eukaryotes with an elaborate spatiotemporal regulation of fundamental molecular processes, such as gene expression and protein translation. Given the highly dynamic nature of nucleocytoplasmic transport, during the past few decades large efforts were devoted to the development and application of time resolved, fluorescence-based, biophysical methods to capture the details of molecular motion across the nuclear envelope. These methods are here divided into three major classes, according to the differences in the way they report on the molecular process of nucleocytoplasmic transport. In detail, the first class encompasses those methods based on the perturbation of the fluorescence signal, also known as ensemble-averaging methods, which average the behavior of many molecules (across many pores). The second class comprises those methods based on the localization of single fluorescently-labelled molecules and tracking of their position in space and time, potentially across single pores. Finally, the third class encompasses methods based on the statistical analysis of spontaneous fluorescence fluctuations out of the equilibrium or stationary state of the system. In this case, the behavior of single molecules is probed in presence of many similarly-labelled molecules, without dwelling on any of them. Here these three classes, with their respective pros and cons as well as their main applications to nucleocytoplasmic shuttling will be briefly reviewed and discussed.
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23
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Zhao ZW, White MD, Bissiere S, Levi V, Plachta N. Quantitative imaging of mammalian transcriptional dynamics: from single cells to whole embryos. BMC Biol 2016; 14:115. [PMID: 28010727 PMCID: PMC5180410 DOI: 10.1186/s12915-016-0331-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Probing dynamic processes occurring within the cell nucleus at the quantitative level has long been a challenge in mammalian biology. Advances in bio-imaging techniques over the past decade have enabled us to directly visualize nuclear processes in situ with unprecedented spatial and temporal resolution and single-molecule sensitivity. Here, using transcription as our primary focus, we survey recent imaging studies that specifically emphasize the quantitative understanding of nuclear dynamics in both time and space. These analyses not only inform on previously hidden physical parameters and mechanistic details, but also reveal a hierarchical organizational landscape for coordinating a wide range of transcriptional processes shared by mammalian systems of varying complexity, from single cells to whole embryos.
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Affiliation(s)
- Ziqing W Zhao
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Melanie D White
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Stephanie Bissiere
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Valeria Levi
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Conicet, Buenos Aires, C1428EHA, Argentina
| | - Nicolas Plachta
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore.
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24
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Presman DM, Hager GL. More than meets the dimer: What is the quaternary structure of the glucocorticoid receptor? Transcription 2016; 8:32-39. [PMID: 27764575 PMCID: PMC5279712 DOI: 10.1080/21541264.2016.1249045] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
It is widely accepted that the glucocorticoid receptor (GR), a ligand-regulated transcription factor that triggers anti-inflammatory responses, binds specific response elements as a homodimer. Here, we will discuss the original primary data that established this model and contrast it with a recent report characterizing the GR-DNA complex as a tetramer.
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Affiliation(s)
- Diego M Presman
- a Laboratory of Receptor Biology and Gene Expression , National Cancer Institute, National Institutes of Health , Bethesda , MD , USA
| | - Gordon L Hager
- a Laboratory of Receptor Biology and Gene Expression , National Cancer Institute, National Institutes of Health , Bethesda , MD , USA
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25
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Gaus K. Biologists Wanted: New Fluorescence Fluctuation Tools for Cell Biology. Biophys J 2016; 111:677-678. [PMID: 27558711 DOI: 10.1016/j.bpj.2016.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 11/28/2022] Open
Affiliation(s)
- Katharina Gaus
- European Molecular Biology Laboratory Australia Node in Single Molecule Science, School of Medical Sciences, Sydney, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia.
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26
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DNA binding triggers tetramerization of the glucocorticoid receptor in live cells. Proc Natl Acad Sci U S A 2016; 113:8236-41. [PMID: 27382178 DOI: 10.1073/pnas.1606774113] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcription factors dynamically bind to chromatin and are essential for the regulation of genes. Although a large percentage of these proteins appear to self-associate to form dimers or higher order oligomers, the stoichiometry of DNA-bound transcription factors has been poorly characterized in vivo. The glucocorticoid receptor (GR) is a ligand-regulated transcription factor widely believed to act as a dimer or a monomer. Using a unique set of imaging techniques coupled with a cell line containing an array of DNA binding elements, we show that GR is predominantly a tetramer when bound to its target DNA. We find that DNA binding triggers an interdomain allosteric regulation within the GR, leading to tetramerization. We therefore propose that dynamic changes in GR stoichiometry represent a previously unidentified level of regulation in steroid receptor activation. Quaternary structure analysis of other members of the steroid receptor family (estrogen, androgen, and progesterone receptors) reveals variation in oligomerization states among this family of transcription factors. Because GR's oligomerization state has been implicated in therapy outcome, our findings open new doors to the rational design of novel GR ligands and redefine the quaternary structure of steroid receptors.
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Gambin Y, Polinkovsky M, Francois B, Giles N, Bhumkar A, Sierecki E. Confocal Spectroscopy to Study Dimerization, Oligomerization and Aggregation of Proteins: A Practical Guide. Int J Mol Sci 2016; 17:ijms17050655. [PMID: 27144560 PMCID: PMC4881481 DOI: 10.3390/ijms17050655] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/15/2016] [Accepted: 04/20/2016] [Indexed: 12/25/2022] Open
Abstract
Protein self-association is a key feature that can modulate the physiological role of proteins or lead to deleterious effects when uncontrolled. Protein oligomerization is a simple way to modify the activity of a protein, as the modulation of binding interfaces allows for self-activation or inhibition, or variation in the selectivity of binding partners. As such, dimerization and higher order oligomerization is a common feature in signaling proteins, for example, and more than 70% of enzymes have the potential to self-associate. On the other hand, protein aggregation can overcome the regulatory mechanisms of the cell and can have disastrous physiological effects. This is the case in a number of neurodegenerative diseases, where proteins, due to mutation or dysregulation later in life, start polymerizing and often fibrillate, leading to the creation of protein inclusion bodies in cells. Dimerization, well-defined oligomerization and random aggregation are often difficult to differentiate and characterize experimentally. Single molecule “counting” methods are particularly well suited to the study of self-oligomerization as they allow observation and quantification of behaviors in heterogeneous conditions. However, the extreme dilution of samples often causes weak complexes to dissociate, and rare events can be overlooked. Here, we discuss a straightforward alternative where the principles of single molecule detection are used at higher protein concentrations to quantify oligomers and aggregates in a background of monomers. We propose a practical guide for the use of confocal spectroscopy to quantify protein oligomerization status and also discuss about its use in monitoring changes in protein aggregation in drug screening assays.
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Affiliation(s)
- Yann Gambin
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Mark Polinkovsky
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Bill Francois
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Nichole Giles
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Akshay Bhumkar
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
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