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Cremer C, Schock F, Failla AV, Birk U. Modulated illumination microscopy: Application perspectives in nuclear nanostructure analysis. J Microsc 2024. [PMID: 38618985 DOI: 10.1111/jmi.13297] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 02/26/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
The structure of the cell nucleus of higher organisms has become a major topic of advanced light microscopy. So far, a variety of methods have been applied, including confocal laser scanning fluorescence microscopy, 4Pi, STED and localisation microscopy approaches, as well as different types of patterned illumination microscopy, modulated either laterally (in the object plane) or axially (along the optical axis). Based on our experience, we discuss here some application perspectives of Modulated Illumination Microscopy (MIM) and its combination with single-molecule localisation microscopy (SMLM). For example, spatially modulated illumination microscopy/SMI (illumination modulation along the optical axis) has been used to determine the axial extension (size) of small, optically isolated fluorescent objects between ≤ 200 nm and ≥ 40 nm diameter with a precision down to the few nm range; it also allows the axial positioning of such structures down to the 1 nm scale; combined with laterally structured illumination/SIM, a 3D localisation precision of ≤1 nm is expected using fluorescence yields typical for SMLM applications. Together with the nanosizing capability of SMI, this can be used to analyse macromolecular nuclear complexes with a resolution approaching that of cryoelectron microscopy.
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Affiliation(s)
- Christoph Cremer
- Kirchhoff Institute for Physics (KIP), Heidelberg, Germany
- Interdisciplinary Centre for Scientific Computing (IWR), University of Heidelberg, Heidelberg, Germany
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Florian Schock
- Kirchhoff Institute for Physics (KIP), Heidelberg, Germany
| | - Antonio Virgilio Failla
- UKE Microscopy Imaging Facility, University Medical Centre Hamburg Eppendorf, Hamburg, Germany
| | - Udo Birk
- Institute for Photonics and Robotics (IPR), Department of Applied Future Technologies, University of Applied Sciences of the Grisons (FH Graubünden), Chur, Switzerland
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2
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Zhu X, Chen Q, Zhao H, Yang Q, Goudappagouda, Gelléri M, Ritz S, Ng D, Koynov K, Parekh SH, Chetty VK, Thakur BK, Cremer C, Landfester K, Müllen K, Terenzio M, Bonn M, Narita A, Liu X. Intrinsic Burst-Blinking Nanographenes for Super-Resolution Bioimaging. J Am Chem Soc 2024; 146:5195-5203. [PMID: 38275287 PMCID: PMC10910517 DOI: 10.1021/jacs.3c11152] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
Single-molecule localization microscopy (SMLM) is a powerful technique to achieve super-resolution imaging beyond the diffraction limit. Although various types of blinking fluorophores are currently considered for SMLM, intrinsic blinking fluorophores remain rare at the single-molecule level. Here, we report the synthesis of nanographene-based intrinsic burst-blinking fluorophores for highly versatile SMLM. We image amyloid fibrils in air and in various pH solutions without any additive and lysosome dynamics in live mammalian cells under physiological conditions. In addition, the single-molecule labeling of nascent proteins in primary sensory neurons was achieved with azide-functionalized nanographenes via click chemistry. SMLM imaging reveals higher local translation at axonal branching with unprecedented detail, while the size of translation foci remained similar throughout the entire network. These various results demonstrate the potential of nanographene-based fluorophores to drastically expand the applicability of super-resolution imaging.
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Affiliation(s)
- Xingfu Zhu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Qiang Chen
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Hao Zhao
- Organic
and Carbon Nanomaterials Unit, Okinawa Institute
of Science and Technology Graduate University, Kunigami-gun, Okinawa 904-0495, Japan
| | - Qiqi Yang
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Goudappagouda
- Organic
and Carbon Nanomaterials Unit, Okinawa Institute
of Science and Technology Graduate University, Kunigami-gun, Okinawa 904-0495, Japan
| | - Márton Gelléri
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Sandra Ritz
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
| | - David Ng
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kaloian Koynov
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sapun H. Parekh
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | | | - Basant Kumar Thakur
- Department
of Pediatrics III, University Hospital Essen, 45147 Essen, Germany
| | - Christoph Cremer
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Katharina Landfester
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Klaus Müllen
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Marco Terenzio
- Molecular
Neuroscience Unit, Okinawa Institute of
Science and Technology Graduate University, Kunigami-gun, Okinawa 904-0495, Japan
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Akimitsu Narita
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Organic
and Carbon Nanomaterials Unit, Okinawa Institute
of Science and Technology Graduate University, Kunigami-gun, Okinawa 904-0495, Japan
| | - Xiaomin Liu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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Gelléri M, Chen SY, Hübner B, Neumann J, Kröger O, Sadlo F, Imhoff J, Hendzel MJ, Cremer M, Cremer T, Strickfaden H, Cremer C. True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin. Cell Rep 2023; 42:112567. [PMID: 37243597 DOI: 10.1016/j.celrep.2023.112567] [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: 06/27/2022] [Revised: 03/02/2023] [Accepted: 05/10/2023] [Indexed: 05/29/2023] Open
Abstract
Chromatin compaction differences may have a strong impact on accessibility of individual macromolecules and macromolecular assemblies to their DNA target sites. Estimates based on fluorescence microscopy with conventional resolution, however, suggest only modest compaction differences (∼2-10×) between the active nuclear compartment (ANC) and inactive nuclear compartment (INC). Here, we present maps of nuclear landscapes with true-to-scale DNA densities, ranging from <5 to >300 Mbp/μm3. Maps are generated from individual human and mouse cell nuclei with single-molecule localization microscopy at ∼20 nm lateral and ∼100 nm axial optical resolution and are supplemented by electron spectroscopic imaging. Microinjection of fluorescent nanobeads with sizes corresponding to macromolecular assemblies for transcription into nuclei of living cells demonstrates their localization and movements within the ANC and exclusion from the INC.
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Affiliation(s)
- Márton Gelléri
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany.
| | - Shih-Ya Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Barbara Hübner
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Jan Neumann
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Ole Kröger
- Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany
| | - Filip Sadlo
- Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany
| | - Jorg Imhoff
- Neuroconsult GmbH, 69120 Heidelberg, Germany
| | - Michael J Hendzel
- Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Marion Cremer
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Thomas Cremer
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Hilmar Strickfaden
- Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Max Planck Institute for Chemistry, 55128 Mainz, Germany; Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany; Kirchhoff Institute for Physics, University Heidelberg, 69120 Heidelberg, Germany.
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Ghanam J, Chetty VK, Zhu X, Liu X, Gelléri M, Barthel L, Reinhardt D, Cremer C, Thakur BK. Single Molecule Localization Microscopy for Studying Small Extracellular Vesicles. Small 2023; 19:e2205030. [PMID: 36635058 DOI: 10.1002/smll.202205030] [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] [Received: 08/16/2022] [Revised: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Small extracellular vesicles (sEVs) are 30-200 nm nanovesicles enriched with unique cargoes of nucleic acids, lipids, and proteins. sEVs are released by all cell types and have emerged as a critical mediator of cell-to-cell communication. Although many studies have dealt with the role of sEVs in health and disease, the exact mechanism of sEVs biogenesis and uptake remain unexplored due to the lack of suitable imaging technologies. For sEVs functional studies, imaging has long relied on conventional fluorescence microscopy that has only 200-300 nm resolution, thereby generating blurred images. To break this resolution limit, recent developments in super-resolution microscopy techniques, specifically single-molecule localization microscopy (SMLM), expanded the understanding of subcellular details at the few nanometer level. SMLM success relies on the use of appropriate fluorophores with excellent blinking properties. In this review, the basic principle of SMLM is highlighted and the state of the art of SMLM use in sEV biology is summarized. Next, how SMLM techniques implemented for cell imaging can be translated to sEV imaging is discussed by applying different labeling strategies to study sEV biogenesis and their biomolecular interaction with the distant recipient cells.
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Affiliation(s)
- Jamal Ghanam
- Department of Pediatrics III, University Hospital Essen, 45147, Essen, Germany
| | | | - Xingfu Zhu
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Xiaomin Liu
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Márton Gelléri
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Lennart Barthel
- Department of Neurosurgery and Spine Surgery, Center for Translational Neuro and Behavioral Sciences, University Hospital Essen, 45147, Essen, Germany
- Institute of Medical Psychology and Behavioral Immunobiology, Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, 45147, Essen, Germany
| | - Dirk Reinhardt
- Department of Pediatrics III, University Hospital Essen, 45147, Essen, Germany
| | - Christoph Cremer
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Basant Kumar Thakur
- Department of Pediatrics III, University Hospital Essen, 45147, Essen, Germany
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Chapman KB, Filipsky F, Peschke N, Gelléri M, Weinhardt V, Braun A, Hausmann M, Cremer C. A comprehensive method to study the DNA's association with lamin and chromatin compaction in intact cell nuclei at super resolution. Nanoscale 2023; 15:742-756. [PMID: 36524744 PMCID: PMC9813922 DOI: 10.1039/d2nr02684h] [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] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
Super-resolution fluorescence microscopy has revolutionized multicolor imaging of nuclear structures due to the combination of high labeling specificity and high resolution. Here we expanded the recently developed fBALM (DNA structure fluctuation-assisted binding activated localization microscopy) method by developing a stable methodological sequence that enables dual-color imaging of high-resolution genomic DNA together with an immunofluorescently labeled intranuclear protein. Our measurements of the nuclear periphery, imaging DNA and LaminB1 in biologically relevant samples, show that this novel dual-color imaging method is feasible for further quantitative evaluations. We were able to study the relative spatial signal organization between DNA and LaminB1 by means of highly specific colocalization measurements at nanometer resolution. Measurements were performed with and without the antifade embedding medium ProLong Gold, which proved to be essential for imaging of LaminB1, but not for imaging of SytoxOrange labeled DNA. The localization precision was used to differentiate between localizations with higher and lower amounts of emitting photons. We interpret high intensity localizations to be renatured DNA sections in which a high amount of Sytox Orange molecules were bound. This could give insight into the denaturation kinetics of DNA during fBALM. These results were further complemented by measurements of γH2AX and H3K9me3 signal organization to demonstrate differences within the chromatin landscape, which were quantified with image processing methods such as Voronoi segmentation.
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Affiliation(s)
- Katarina B Chapman
- Kirchhoff-Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany.
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Filip Filipsky
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Nicolas Peschke
- Kirchhoff-Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany.
| | - Márton Gelléri
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Venera Weinhardt
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Andrejs Braun
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany.
| | - Christoph Cremer
- Kirchhoff-Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany.
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
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6
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Chetty VK, Ghanam J, Anchan S, Reinhardt K, Brenzel A, Gelléri M, Cremer C, Grueso-Navarro E, Schneider M, von Neuhoff N, Reinhardt D, Jablonska J, Nazarenko I, Thakur BK. Efficient Small Extracellular Vesicles (EV) Isolation Method and Evaluation of EV-Associated DNA Role in Cell-Cell Communication in Cancer. Cancers (Basel) 2022; 14:cancers14092068. [PMID: 35565197 PMCID: PMC9099953 DOI: 10.3390/cancers14092068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Small extracellular vesicles (sEVs) released by all cell types function as a mediator in intercellular communication that can promote cell division and survival to remodel the tumor microenvironment to develop tumor invasion and metastasis. Even though dsDNA baggage is associated with all small EV populations, the functional role of EV-DNA in cancer remains poorly understood. This is due to a lack of methods allowing the efficient separation of small EVs (sEVs) from other non-sEV components. The main aim of our study was to develop an efficient sEV isolation method along with EV-associated DNA (EV-DNA) monitoring tool to evaluate the role of EV-DNA as a mediator of cell–cell communication in cancer. Our detailed small EV-DNA characterization confirmed that isolated sEVs using the TSU method (Tangential flow filtration + Size exclusion chromatography + Ultrafiltration) are free from contaminants such as cell-free and apoptotic bodies DNA, making TSU ideal for performing EV-DNA functional studies. Next, we revealed the exact EV-DNA distribution in the recipient cells using 3D image analysis and the association of EV-DNA with key cellular proteins, which may have an essential role in cancer. In the leukemia model, EV-DNA isolated from leukemia cell lines associated with mesenchymal stromal cells (MSCs), a crucial factor in the bone marrow (BM) microenvironment. Abstract Small extracellular vesicles (sEVs) play essential roles in intercellular signaling both in normal and pathophysiological conditions. Comprehensive studies of dsDNA associated with sEVs are hampered by a lack of methods, allowing efficient separation of sEVs from free-circulating DNA and apoptotic bodies. In this work, using controlled culture conditions, we enriched the reproducible separation of sEVs from free-circulated components by combining tangential flow filtration, size-exclusion chromatography, and ultrafiltration (TSU). EV-enriched fractions (F2 and F3) obtained using TSU also contained more dsDNA derived from the host genome and mitochondria, predominantly localized inside the vesicles. Three-dimensional reconstruction of high-resolution imaging showed that the recipient cell membrane barrier restricts a portion of EV-DNA. Simultaneously, the remaining EV-DNA overcomes it and enters the cytoplasm and nucleus. In the cytoplasm, EV-DNA associates with dsDNA-inflammatory sensors (cGAS/STING) and endosomal proteins (Rab5/Rab7). Relevant to cancer, we found that EV-DNA isolated from leukemia cell lines communicates with mesenchymal stromal cells (MSCs), a critical component in the BM microenvironment. Furthermore, we illustrated the arrangement of sEVs and EV-DNA at a single vesicle level using super-resolution microscopy. Altogether, employing TSU isolation, we demonstrated EV-DNA distribution and a tool to evaluate the exact EV-DNA role of cell–cell communication in cancer.
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Affiliation(s)
- Venkatesh Kumar Chetty
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Jamal Ghanam
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Srishti Anchan
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Katarina Reinhardt
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Alexandra Brenzel
- Imaging Center Essen (IMCES), University Hospital Essen, 45147 Essen, Germany;
| | - Márton Gelléri
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; (M.G.); (C.C.)
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; (M.G.); (C.C.)
- Max Planck Institutes for Polymer Research and for Chemistry, 55128 Mainz, Germany
| | - Elena Grueso-Navarro
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, 79106 Freiburg, Germany; (E.G.-N.); (I.N.)
| | - Markus Schneider
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Nils von Neuhoff
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Dirk Reinhardt
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Jadwiga Jablonska
- Department of Otorhinolaryngology, University Hospital Essen, 45147 Essen, Germany;
| | - Irina Nazarenko
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, 79106 Freiburg, Germany; (E.G.-N.); (I.N.)
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Basant Kumar Thakur
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
- Correspondence: ; Tel.: +49-201-723-2504
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7
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Cremer C, Birk U. Spatially modulated illumination microscopy: application perspectives in nuclear nanostructure analysis. Phil Trans R Soc A 2022; 380:20210152. [PMID: 0 DOI: 10.1098/rsta.2021.0152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/02/2021] [Indexed: 05/19/2023]
Abstract
Thousands of genes and the complex biochemical networks for their transcription are packed in the micrometer sized cell nucleus. To control biochemical processes, spatial organization plays a key role. Hence the structure of the cell nucleus of higher organisms has emerged as a main topic of advanced light microscopy. So far, a variety of methods have been applied for this, including confocal laser scanning fluorescence microscopy, 4Pi-, STED- and localization microscopy approaches, as well as (laterally) structured illumination microscopy (SIM). Here, we summarize the state of the art and discuss application perspectives for nuclear nanostructure analysis of spatially modulated illumination (SMI). SMI is a widefield-based approach to using axially structured illumination patterns to determine the axial extension (size) of small, optically isolated fluorescent objects between less than or equal to 200 nm and greater than or equal to 40 nm diameter with a precision down to the few nm range; in addition, it allows the axial positioning of such structures down to the 1 nm scale. Combined with SIM, a three-dimensional localization precision of less than or equal to 1 nm is expected to become feasible using fluorescence yields typical for single molecule localization microscopy applications. Together with its nanosizing capability, this may eventually be used to analyse macromolecular complexes and other nanostructures with a topological resolution, further narrowing the gap to Cryoelectron microscopy.
This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 2)’.
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Affiliation(s)
- Christoph Cremer
- Max-Planck Institute for Polymer Research, and Institute of Molecular Biology (IMB), D-55128 Mainz, Germany
- Kirchhoff Institute for Physics (KIP), Interdisciplinary Center for Scientific Computing (IWR), and Institute of Pharmacy and Molecular Biotechnology (IPMB), University Heidelberg, D-69120 Heidelberg, Germany
| | - Udo Birk
- Institute for Photonics and ICT (IPI), University of Applied Sciences (FH Graubünden), CH-7000 Chur, Switzerland
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8
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Schock F, Best G, Celik N, Heintzmann R, Dithmar S, Cremer C. Structured illumination ophthalmoscope: super-resolution microscopy on the living human eye. Phil Trans R Soc A 2022; 380:20210151. [PMID: 0 DOI: 10.1098/rsta.2021.0151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/15/2022] [Indexed: 05/19/2023]
Abstract
In this paper, we present the prototype of an ophthalmoscope that uses structured illumination microscopy (SIM) to enable super-resolved imaging of the human retina, and give first insights into clinical application possibilities. The SIM technique was applied to build a prototype that uses the lens of the human eye as an objective to ‘super-resolve’ the retina of a living human. In our multidisciplinary collaboration, we have adapted this well-established technique in ophthalmology and successfully imaged a human retina using significantly lower light intensity than a state-of-the-art ophthalmoscope. Here, we focus on the technical implementation and highlight future perspectives of this method. A more application-oriented note for physicians on the diagnostic and disease-preventive value of this method, as well as the medical results of the clinical study carried out, will be published in a report addressed to an appropriate specialist audience.
This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 2)’.
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Affiliation(s)
- Florian Schock
- Institute of Physics, Johannes Gutenberg University Mainz, Mainz, Germany
- Kirchhoff-Institute for Physics, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Gerrit Best
- Kirchhoff-Institute for Physics, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
- Department of Ophthalmology, University of Heidelberg, Heidelberg, Germany
| | - Nil Celik
- Department of Ophthalmology, University of Heidelberg, Heidelberg, Germany
| | - Rainer Heintzmann
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Jena, Germany
- Leibniz Institute of Photonic Technology, Jena, Germany
| | - Stefan Dithmar
- Department of Ophthalmology, HELIOS-HSK, Wiesbaden, Germany
- Department of Ophthalmology, University of Heidelberg, Heidelberg, Germany
| | - Christoph Cremer
- Institute of Physics, Johannes Gutenberg University Mainz, Mainz, Germany
- Kirchhoff-Institute for Physics, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
- Max Planck Institute for Polymer Research, Mainz, Germany
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9
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Lang F, Contreras-Gerenas MF, Gelléri M, Neumann J, Kröger O, Sadlo F, Berniak K, Marx A, Cremer C, Wagenknecht HA, Allgayer H. Tackling Tumour Cell Heterogeneity at the Super-Resolution Level in Human Colorectal Cancer Tissue. Cancers (Basel) 2021; 13:cancers13153692. [PMID: 34359592 PMCID: PMC8345115 DOI: 10.3390/cancers13153692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Tumour cell heterogeneity is the most fundamental problem in cancer diagnosis and therapy. Micro-diagnostic technologies able to differentiate the heterogeneous molecular, especially metastatic, potential of single cells or cell clones already within early primary tumours of carcinoma patients would be of utmost importance. Single molecule localisation microscopy (SMLM) has recently allowed the imaging of subcellular features at the nanoscale. However, the technology has mostly been limited to cultured cell lines only. We introduce a first-in-field approach for quantitative SMLM-analysis of chromatin nanostructure in individual cells in resected, routine-pathology colorectal carcinoma patient tissue sections, illustrating, as a first example, changes in nuclear chromatin nanostructure and microRNA intracellular distribution within carcinoma cells as opposed to normal cells, chromatin accessibility and microRNAs having been shown to be critical in gene regulation and metastasis. We believe this technology to have an enormous potential for future differential diagnosis between individual cells in the tissue context. Abstract Tumour cell heterogeneity, and its early individual diagnosis, is one of the most fundamental problems in cancer diagnosis and therapy. Single molecule localisation microscopy (SMLM) resolves subcellular features but has been limited to cultured cell lines only. Since nuclear chromatin architecture and microRNAs are critical in metastasis, we introduce a first-in-field approach for quantitative SMLM-analysis of chromatin nanostructure in individual cells in resected, routine-pathology colorectal carcinoma (CRC) patient tissue sections. Chromatin density profiles proved to differ for cells in normal and carcinoma colorectal tissues. In tumour sections, nuclear size and chromatin compaction percentages were significantly different in carcinoma versus normal epithelial and other cells of colorectal tissue. SMLM analysis in nuclei from normal colorectal tissue revealed abrupt changes in chromatin density profiles at the nanoscale, features not detected by conventional widefield microscopy. SMLM for microRNAs relevant for metastasis was achieved in colorectal cancer tissue at the nuclear level. Super-resolution microscopy with quantitative image evaluation algorithms provide powerful tools to analyse chromatin nanostructure and microRNAs of individual cells from normal and tumour tissue at the nanoscale. Our new perspectives improve the differential diagnosis of normal and (metastatically relevant) tumour cells at the single-cell level within the heterogeneity of primary tumours of patients.
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Affiliation(s)
- Fabian Lang
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, Campus Süd, 76131 Karlsruhe, Germany; (F.L.); (H.-A.W.)
| | - María F. Contreras-Gerenas
- Department of Experimental Surgery—Cancer Metastasis, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany;
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Márton Gelléri
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Jan Neumann
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
| | - Ole Kröger
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
| | - Filip Sadlo
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
| | - Krzysztof Berniak
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7 Street, 30-387 Krakow, Poland;
| | - Alexander Marx
- Institute of Pathology, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Theodor-Kutzer-Ufer 1, 68167 Mannheim, Germany;
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; (M.G.); (J.N.); (C.C.)
- Interdisciplinary Centre for Scientific Computing (IWR), University Heidelberg, Mathematikon B, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany; (O.K.); (F.S.)
- Institute of Pharmacy & Molecular Biotechnology, Ruprecht-Karls University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, Campus Süd, 76131 Karlsruhe, Germany; (F.L.); (H.-A.W.)
| | - Heike Allgayer
- Department of Experimental Surgery—Cancer Metastasis, Mannheim Medical Faculty, Ruprecht-Karls University of Heidelberg, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany;
- Correspondence: ; Tel.: +49-(0)621-383-71630/-1406/-71635; Fax: +49-(0)621-383-71631
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Popp S, Remm B, Hausmann M, Lührs H, Kaick GV, Cremer T, Cremer C. Towards a cumulative biological dosimeter based on chromosome painting and digital image analysis / Zur Entwicklung eines biologischen Langzeitdosimeters mittels chromosomaler In-situ-Suppressions-Hybridisierung und automatischer Bildanalyse. KERNTECHNIK 2021. [DOI: 10.1515/kern-1990-550407] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Abplanalp W, Cremer C, Cremer S, John D, John D, Hoffmann J, Hoffmann J, Rieger M, Rieger M, Vasa-Nicotera M, Vasa-Nicotera M, Zeiher A, Zeiher A, Dimmeler S, Dimmeler S. DNMT3A clonal hematopoiesis-driver mutations are associated with profound changes in monocyte and T cell signatures in humans with heart failure. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.3626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Clonal hematopoiesis (CH) driven by mutations of DNA methyltransferase 3a (DNMT3A) is associated with increased incidence of cardiovascular disease and poor prognosis of patients with chronic heart failure (HF) and aortic stenosis. Although experimental studies suggest that DNMT3A CH-driver mutations may enhance inflammation, specific signatures of inflammatory cells in humans are missing. Single-cell RNA-sequencing provides a novel opportunity to define subsets of immune cells mediating inflammation in humans.
Methods
Transcriptomic profiles of peripheral blood mononuclear cells were analysed in N=6 HF patients harboring DNMT3A CH-drived mutations and with HF and N=5 patients with HF and DNMT3A mutations by single-cell RNA-sequencing.
Results
Monocytes of HF patients carrying DNMT3A mutations demonstrated a significantly increased expression of inflammatory genes compared to monocytes derived from patients with HF without DNMT3A mutations. Among the specific up-regulated genes were the prototypic inflammatory interleukins (IL) IL1B, IL6, and IL8, the macrophage inflammatory proteins CCL3 and CCL4 as well as restin, which augments monocyte-endothelial adhesion. The classical monocyte subset of DNMT3A mutation carriers showed increased expression of immunoglobulin superfamily members CD80, CD300LB, and SIGLEC12, as well as the cell adhesion molecule CD58, all of which may be involved in monocyte-T cell interactions. DNMT3A mutation carriers were further characterized by increased expression of T cell receptor chains and Th1, Th17, CD8+ and Treg specific signatures.
Conclusions
This study demonstrates that circulating monocytes and T cells of HF patients harboring CHIP-driver mutations in DNMT3A exhibit a highly inflamed transcriptome, which may contribute to the aggravation of chronic heart failure.
Funding Acknowledgement
Type of funding source: Public Institution(s). Main funding source(s): The German Research Foundation (SFB834, Project B1), and the German Center for Cardiovascular Research (DZHK).
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Affiliation(s)
- W Abplanalp
- Wolfgang Goethe University, Frankfurt am Main, Germany
| | - C Cremer
- Wolfgang Goethe University, Frankfurt am Main, Germany
| | - S Cremer
- Wolfgang Goethe University, Frankfurt am Main, Germany
| | - D John
- Wolfgang Goethe University, Frankfurt am Main, Germany
| | - D John
- Wolfgang Goethe University, Frankfurt am Main, Germany
| | - J Hoffmann
- Wolfgang Goethe University, Frankfurt am Main, Germany
| | - J Hoffmann
- Wolfgang Goethe University, Frankfurt am Main, Germany
| | - M.A Rieger
- Wolfgang Goethe University, Frankfurt am Main, Germany
| | - M.A Rieger
- Wolfgang Goethe University, Frankfurt am Main, Germany
| | | | | | - A.M Zeiher
- Wolfgang Goethe University, Frankfurt am Main, Germany
| | - A.M Zeiher
- Wolfgang Goethe University, Frankfurt am Main, Germany
| | - S Dimmeler
- Wolfgang Goethe University, Frankfurt am Main, Germany
| | - S Dimmeler
- Wolfgang Goethe University, Frankfurt am Main, Germany
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Cremer T, Cremer M, Hübner B, Silahtaroglu A, Hendzel M, Lanctôt C, Strickfaden H, Cremer C. The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus. Bioessays 2020; 42:e1900132. [PMID: 31994771 DOI: 10.1002/bies.201900132] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/24/2019] [Indexed: 12/11/2022]
Abstract
This article focuses on the role of the interchromatin compartment (IC) in shaping nuclear landscapes. The IC is connected with nuclear pore complexes (NPCs) and harbors splicing speckles and nuclear bodies. It is postulated that the IC provides routes for imported transcription factors to target sites, for export routes of mRNA as ribonucleoproteins toward NPCs, as well as for the intranuclear passage of regulatory RNAs from sites of transcription to remote functional sites (IC hypothesis). IC channels are lined by less-compacted euchromatin, called the perichromatin region (PR). The PR and IC together form the active nuclear compartment (ANC). The ANC is co-aligned with the inactive nuclear compartment (INC), comprising more compacted heterochromatin. It is postulated that the INC is accessible for individual transcription factors, but inaccessible for larger macromolecular aggregates (limited accessibility hypothesis). This functional nuclear organization depends on still unexplored movements of genes and regulatory sequences between the two compartments.
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Affiliation(s)
- Thomas Cremer
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Marion Cremer
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Barbara Hübner
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Asli Silahtaroglu
- Department of Cellular and Molecular Medicine Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Byg.18.03, 2200, Copenhagen N, Denmark
| | - Michael Hendzel
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Christian Lanctôt
- Integration Santé, 1250 Avenue de la Station local 2-304, Shawinigan, Québec, G9N 8K9, Canada
| | - Hilmar Strickfaden
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Christoph Cremer
- Institute of Molecular Biology (IMB) Ackermannweg 4, 55128 Mainz, Germany, and Institute of Pharmacy & Molecular Biotechnology (IPMB), University Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
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Liu X, Chen S, Chen Q, Yao X, Gelléri M, Ritz S, Kumar S, Cremer C, Landfester K, Müllen K, Parekh SH, Narita A, Bonn M. Back Cover: Nanographenes: Ultrastable, Switchable, and Bright Probes for Super‐Resolution Microscopy (Angew. Chem. Int. Ed. 1/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/anie.201915125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaomin Liu
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
| | - Shih‐Ya Chen
- Institute of Molecular Biology gGmbH (IMB) Mainz Germany
| | - Qiang Chen
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
| | - Xuelin Yao
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
| | - Márton Gelléri
- Institute of Molecular Biology gGmbH (IMB) Mainz Germany
| | - Sandra Ritz
- Institute of Molecular Biology gGmbH (IMB) Mainz Germany
| | - Sachin Kumar
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
- Department of Biomedical Engineering University of Texas at Austin Austin TX USA
| | - Christoph Cremer
- Institute of Molecular Biology gGmbH (IMB) Mainz Germany
- Department of Physics University of Mainz (JGU) Mainz Germany
- Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP) University of Heidelberg Heidelberg Germany
| | | | - Klaus Müllen
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
- Institute of Physical Chemistry Johannes Gutenberg-University Mainz Mainz Germany
| | - Sapun H. Parekh
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
- Department of Biomedical Engineering University of Texas at Austin Austin TX USA
| | - Akimitsu Narita
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
- Organic and Carbon Nanomaterials Unit Okinawa Institute of Science and Technology Graduate University Okinawa Japan
| | - Mischa Bonn
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany
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Liu X, Chen S, Chen Q, Yao X, Gelléri M, Ritz S, Kumar S, Cremer C, Landfester K, Müllen K, Parekh SH, Narita A, Bonn M. Rücktitelbild: Nanographene: ultrastabile, schaltbare und helle Sonden für die hochauflösende Mikroskopie (Angew. Chem. 1/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaomin Liu
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Shih‐Ya Chen
- Institut für Molekularbiologie gGmbH (IMB) Mainz Deutschland
| | - Qiang Chen
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Xuelin Yao
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Márton Gelléri
- Institut für Molekularbiologie gGmbH (IMB) Mainz Deutschland
| | - Sandra Ritz
- Institut für Molekularbiologie gGmbH (IMB) Mainz Deutschland
| | - Sachin Kumar
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
- Department of Biomedical Engineering University of Texas at Austin Austin TX USA
| | - Christoph Cremer
- Institut für Molekularbiologie gGmbH (IMB) Mainz Deutschland
- Physikalisches Institut Universität Mainz (JGU) Mainz Deutschland
- Institut für Pharmazie und Molekulare Biotechnologie (IPMB), und Kirchhoff-Institut für Physik (KIP) Universität Heidelberg Heidelberg Deutschland
| | - Katharina Landfester
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Klaus Müllen
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
- Institut für Physikalische Chemie Johannes Gutenberg-Universität Mainz Mainz Deutschland
| | - Sapun H. Parekh
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
- Department of Biomedical Engineering University of Texas at Austin Austin TX USA
| | - Akimitsu Narita
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
- Organic and Carbon Nanomaterials Unit Okinawa Institute of Science and Technology Graduate University Okinawa Japan
| | - Mischa Bonn
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
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Chen SY, Heintzmann R, Cremer C. Sample drift estimation method based on speckle patterns formed by backscattered laser light. Biomed Opt Express 2019; 10:6462-6475. [PMID: 31853411 PMCID: PMC6913400 DOI: 10.1364/boe.10.006462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 05/06/2023]
Abstract
Single molecule localization microscopy (SMLM) has been established to acquire images with unprecedented resolution down to several nanometers. A typical time scale for image acquisition is several minutes to hours. Yet it is difficult to avoid completely sample drift for long time measurements. To estimate drift, we present a method based on the evaluation of speckle patterns formed by backscattered laser light from the cells using a single molecule localization microscope setup. A z-stack of unique speckle patterns is recorded prior to the measurements as a three-dimensional position reference. During the experiment, images of scattered laser light were acquired, and correlated individually with each of the images of the speckle reference stack to estimate x, y and z drift. Our method shows highly comparable results with a fiducial marker approach, achieving a precision of several nanometers. This method allows for high precision three dimensional drift correction of microscope systems without any additional sample preparation.
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Affiliation(s)
| | - Rainer Heintzmann
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology, Jena, Germany
| | - Christoph Cremer
- Institute of Molecular Biology, Mainz, Germany
- Department of Physics, University of Mainz (JGU), Mainz, Germany
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Liu X, Chen SY, Chen Q, Yao X, Gelléri M, Ritz S, Kumar S, Cremer C, Landfester K, Müllen K, Parekh SH, Narita A, Bonn M. Nanographenes: Ultrastable, Switchable, and Bright Probes for Super-Resolution Microscopy. Angew Chem Int Ed Engl 2019; 59:496-502. [PMID: 31657497 PMCID: PMC6972658 DOI: 10.1002/anie.201909220] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Indexed: 01/03/2023]
Abstract
Super‐resolution fluorescence microscopy has enabled important breakthroughs in biology and materials science. Implementations such as single‐molecule localization microscopy (SMLM) and minimal emission fluxes (MINFLUX) microscopy in the localization mode exploit fluorophores that blink, i.e., switch on and off, stochastically. Here, we introduce nanographenes, namely large polycyclic aromatic hydrocarbons that can also be regarded as atomically precise graphene quantum dots, as a new class of fluorophores for super‐resolution fluorescence microscopy. Nanographenes exhibit outstanding photophysical properties: intrinsic blinking even in air, excellent fluorescence recovery, and stability over several months. As a proof of concept for super‐resolution applications, we use nanographenes in SMLM to generate 3D super‐resolution images of silica nanocracks. Our findings open the door for the widespread application of nanographenes in super‐resolution fluorescence microscopy.
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Affiliation(s)
- Xiaomin Liu
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Shih-Ya Chen
- Institute of Molecular Biology gGmbH (IMB), Mainz, Germany
| | - Qiang Chen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Xuelin Yao
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Márton Gelléri
- Institute of Molecular Biology gGmbH (IMB), Mainz, Germany
| | - Sandra Ritz
- Institute of Molecular Biology gGmbH (IMB), Mainz, Germany
| | - Sachin Kumar
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Christoph Cremer
- Institute of Molecular Biology gGmbH (IMB), Mainz, Germany.,Department of Physics, University of Mainz (JGU), Mainz, Germany.,Institute for Pharmacy and Molecular Biotechnology (IPMB), and, Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Klaus Müllen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Institute of Physical Chemistry, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Sapun H Parekh
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Akimitsu Narita
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Organic and Carbon Nanomaterials Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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Liu X, Chen S, Chen Q, Yao X, Gelléri M, Ritz S, Kumar S, Cremer C, Landfester K, Müllen K, Parekh SH, Narita A, Bonn M. Nanographene: ultrastabile, schaltbare und helle Sonden für die hochauflösende Mikroskopie. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Xiaomin Liu
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Shih‐Ya Chen
- Institut für Molekularbiologie gGmbH (IMB) Mainz Deutschland
| | - Qiang Chen
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Xuelin Yao
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Márton Gelléri
- Institut für Molekularbiologie gGmbH (IMB) Mainz Deutschland
| | - Sandra Ritz
- Institut für Molekularbiologie gGmbH (IMB) Mainz Deutschland
| | - Sachin Kumar
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
- Department of Biomedical Engineering University of Texas at Austin Austin TX USA
| | - Christoph Cremer
- Institut für Molekularbiologie gGmbH (IMB) Mainz Deutschland
- Physikalisches Institut Universität Mainz (JGU) Mainz Deutschland
- Institut für Pharmazie und Molekulare Biotechnologie (IPMB), und Kirchhoff-Institut für Physik (KIP) Universität Heidelberg Heidelberg Deutschland
| | - Katharina Landfester
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Klaus Müllen
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
- Institut für Physikalische Chemie Johannes Gutenberg-Universität Mainz Mainz Deutschland
| | - Sapun H. Parekh
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
- Department of Biomedical Engineering University of Texas at Austin Austin TX USA
| | - Akimitsu Narita
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
- Organic and Carbon Nanomaterials Unit Okinawa Institute of Science and Technology Graduate University Okinawa Japan
| | - Mischa Bonn
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
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Szczurek A, Birk U, Knecht H, Dobrucki J, Mai S, Cremer C. Super-resolution binding activated localization microscopy through reversible change of DNA conformation. Nucleus 2019; 9:182-189. [PMID: 29297245 PMCID: PMC5973136 DOI: 10.1080/19491034.2017.1419846] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine.
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Affiliation(s)
- Aleksander Szczurek
- a Institute of Molecular Biology , Mainz , Germany.,b Department of Cell Biophysics , Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland
| | - Udo Birk
- a Institute of Molecular Biology , Mainz , Germany.,c Physics Department University of Mainz (JGU) , Mainz , Germany
| | - Hans Knecht
- d McGill, Jewish General Hospital , Montreal , Quebec , Canada
| | - Jurek Dobrucki
- b Department of Cell Biophysics , Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland
| | - Sabine Mai
- e University of Manitoba, Cancer Care Manitoba , Winnipeg , Canada
| | - Christoph Cremer
- a Institute of Molecular Biology , Mainz , Germany.,c Physics Department University of Mainz (JGU) , Mainz , Germany.,f Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University , Germany
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De Backer G, Jankowski P, Kotseva K, Mirrakhimov E, Reiner Ž, Rydén L, Tokgözoğlu L, Wood D, De Bacquer D, De Backer G, Jankowski P, Kotseva K, Mirrakhimov E, Reiner Z, Rydén L, Tokgözoğlu L, Wood D, De Bacquer D, Kotseva K, De Backer G, Abreu A, Aguiar C, Badariene J, Bruthans J, Castro Conde A, Cifkova R, Crowley J, Davletov K, Bacquer DD, De Smedt D, De Sutter J, Deckers J, Dilic M, Dolzhenko M, Druais H, Dzerve V, Erglis A, Fras Z, Gaita D, Gotcheva N, Grobbee D, Gyberg V, Hasan Ali H, Heuschmann P, Hoes A, Jankowski P, Lalic N, Lehto S, Lovic D, Maggioni A, Mancas S, Marques-Vidal P, Mellbin L, Miličić D, Mirrakhimov E, Oganov R, Pogosova N, Reiner Ž, Rydén L, Stagmo M, Störk S, Sundvall J, Tokgözoğlu L, Tsioufis K, Vulic D, Wood D, Wood D, Kotseva K, Jennings C, Adamska A, Adamska S, Rydén L, Mellbin L, Tuomilehto J, Schnell O, Druais H, Fiorucci E, Glemot M, Larras F, Missiamenou V, Maggioni A, Taylor C, Ferreira T, Lemaitre K, Bacquer DD, De Backer G, Raman L, Sundvall J, DeSmedt D, De Sutter J, Willems A, De Pauw M, Vervaet P, Bollen J, Dekimpe E, Mommen N, Van Genechten G, Dendale P, Bouvier C, Chenu P, Huyberechts D, Persu A, Dilic M, Begic A, Durak Nalbantic A, Dzubur A, Hadzibegic N, Iglica A, Kapidjic S, Osmanagic Bico A, Resic N, Sabanovic Bajramovic N, Zvizdic F, Vulic D, Kovacevic-Preradovic T, Popovic-Pejicic S, Djekic D, Gnjatic T, Knezevic T, Kovacevic-Preradovic T, Kos L, Popovic-Pejicic S, Stanetic B, Topic G, Gotcheva N, Georgiev B, Terziev A, Vladimirov G, Angelov A, Kanazirev B, Nikolaeva S, Tonkova D, Vetkova M, Milicic D, Reiner Ž, Bosnic A, Dubravcic M, Glavina M, Mance M, Pavasovic S, Samardzic J, Batinic T, Crljenko K, Delic-Brkljacic D, Dula K, Golubic K, Klobucar I, Kordic K, Kos N, Nedic M, Olujic D, Sedinic V, Blazevic T, Pasalic A, Percic M, Sikic J, Bruthans J, Cífková R, Hašplová K, Šulc P, Wohlfahrt P, Mayer O, Cvíčela M, Filipovský J, Gelžinský J, Hronová M, Hasan-Ali H, Bakery S, Mosad E, Hamed H, Ibrahim A, Elsharef M, Kholef E, Shehata A, Youssef M, Elhefny E, Farid H, Moustafa T, Sobieh M, Kabil H, Abdelmordy A, Lehto S, Kiljander E, Kiljander P, Koukkunen H, Mustonen J, Cremer C, Frantz S, Haupt A, Hofmann U, Ludwig K, Melnyk H, Noutsias M, Karmann W, Prondzinsky R, Herdeg C, Hövelborn T, Daaboul A, Geisler T, Keller T, Sauerbrunn D, Walz-Ayed M, Ertl G, Leyh R, Störk S, Heuschmann P, Ehlert T, Klocke B, Krapp J, Ludwig T, Käs J, Starke C, Ungethüm K, Wagner M, Wiedmann S, Tsioufis K, Tolis P, Vogiatzi G, Sanidas E, Tsakalis K, Kanakakis J, Koutsoukis A, Vasileiadis K, Zarifis J, Karvounis C, Crowley J, Gibson I, Houlihan A, Kelly C, O'Donnell M, Bennati M, Cosmi F, Mariottoni B, Morganti M, Cherubini A, Di Lenarda A, Radini D, Ramani F, Francese M, Gulizia M, Pericone D, Davletov K, Aigerim K, Zholdin B, Amirov B, Assembekov B, Chernokurova E, Ibragimova F, Kodasbayev A, Markova A, Mirrakhimov E, Asanbaev A, Toktomamatov U, Tursunbaev M, Zakirov U, Abilova S, Arapova R, Bektasheva E, Esenbekova J, Neronova K, Asanbaev A, Baigaziev K, Toktomamatov U, Zakirov U, Baitova G, Zheenbekov T, Erglis A, Andrejeva T, Bajare I, Kucika G, Labuce A, Putane L, Stabulniece M, Dzerve V, Klavins E, Sime I, Badariene J, Gedvilaite L, Pečiuraite D, Sileikienė V, Skiauteryte E, Solovjova S, Sidabraite R, Briedis K, Ceponiene I, Jurenas M, Kersulis J, Martinkute G, Vaitiekiene A, Vasiljevaite K, Veisaite R, Plisienė J, Šiurkaitė V, Vaičiulis Ž, Jankowski P, Czarnecka D, Kozieł P, Podolec P, Nessler J, Gomuła P, Mirek-Bryniarska E, Bogacki P, Wiśniewski A, Pająk A, Wolfshaut-Wolak R, Bućko J, Kamiński K, Łapińska M, Paniczko M, Raczkowski A, Sawicka E, Stachurska Z, Szpakowicz M, Musiał W, Dobrzycki S, Bychowski J, Kosior D, Krzykwa A, Setny M, Kosior D, Rak A, Gąsior Z, Haberka M, Gąsior Z, Haberka M, Szostak-Janiak K, Finik M, Liszka J, Botelho A, Cachulo M, Sousa J, Pais A, Aguiar C, Durazzo A, Matos D, Gouveia R, Rodrigues G, Strong C, Guerreiro R, Aguiar J, Abreu A, Cruz M, Daniel P, Morais L, Moreira R, Rosa S, Rodrigues I, Selas M, Gaita D, Mancas S, Apostu A, Cosor O, Gaita L, Giurgiu L, Hudrea C, Maximov D, Moldovan B, Mosteoru S, Pleava R, Ionescu M, Parepa I, Pogosova N, Arutyunov A, Ausheva A, Isakova S, Karpova A, Salbieva A, Sokolova O, Vasilevsky A, Pozdnyakov Y, Antropova O, Borisova L, Osipova I, Lovic D, Aleksic M, Crnokrak B, Djokic J, Hinic S, Vukasin T, Zdravkovic M, Lalic N, Jotic A, Lalic K, Lukic L, Milicic T, Macesic M, Stanarcic Gajovic J, Stoiljkovic M, Djordjevic D, Kostic S, Tasic I, Vukovic A, Fras Z, Jug B, Juhant A, Krt A, Kugonjič U, Chipayo Gonzales D, Gómez Barrado J, Kounka Z, Marcos Gómez G, Mogollón Jiménez M, Ortiz Cortés C, Perez Espejo P, Porras Ramos Y, Colman R, Delgado J, Otero E, Pérez A, Fernández-Olmo M, Torres-LLergo J, Vasco C, Barreñada E, Botas J, Campuzano R, González Y, Rodrigo M, de Pablo C, Velasco E, Hernández S, Lozano C, González P, Castro A, Dalmau R, Hernández D, Irazusta F, Vélez A, Vindel C, Gómez-Doblas J, García Ruíz V, Gómez L, Gómez García M, Jiménez-Navarro M, Molina Ramos A, Marzal D, Martínez G, Lavado R, Vidal A, Rydén L, Boström-Nilsson V, Kjellström B, Shahim B, Smetana S, Hansen O, Stensgaard-Nake E, Deckers J, Klijn A, Mangus T, Peters R, Scholte op Reimer W, Snaterse M, Aydoğdu S, Ç Erol, Otürk S, Tulunay Kaya C, Ahmetoğlu Y, Ergene O, Akdeniz B, Çırgamış D, Akkoyun H Kültürsay S, Kayıkçıoğlu M, Çatakoğlu A, Çengel A, Koçak A, Ağırbaşlı M, Açıksarı G, Çekin M, Tokgözoğlu L, Kaya E, Koçyiğit D, Öngen Z, Özmen E, Sansoy V, Kaya A, Oktay V, Temizhan A, Ünal S, İ Yakut, Kalkan A, Bozkurt E, Kasapkara H, Dolzhenko M, Faradzh C, Hrubyak L, Konoplianyk L, Kozhuharyova N, Lobach L, Nesukai V, Nudchenko O, Simagina T, Yakovenko L, Azarenko V, Potabashny V, Bazylevych A, Bazylevych M, Kaminska K, Panchenko L, Shershnyova O, Ovrakh T, Serik S, Kolesnik T, Kosova H, Wood D, Adamska A, Adamska S, Jennings C, Kotseva K, Hoye P Atkin A, Fellowes D, Lindsay S, Atkinson C, Kranilla C, Vinod M, Beerachee Y, Bennett C, Broome M, Bwalya A, Caygill L, Dinning L, Gillespie A, Goodfellow R, Guy J, Idress T, Mills C, Morgan C, Oustance N, Singh N, Yare M, Jagoda J, Bowyer H, Christenssen V, Groves A, Jan A, Riaz A, Gill M, Sewell T, Gorog D, Baker M, De Sousa P, Mazenenga T, Porter J, Haines F, Peachey T, Taaffe J, Wells K, Ripley D, Forward H, McKie H, Pick S, Thomas H, Batin P, Exley D, Rank T, Wright J, Kardos A, Sutherland SB, Wren L, Leeson P, Barker D, Moreby B, Sawyer J, Stirrup J, Brunton M, Brodison A, Craig J, Peters S, Kaprielian R, Bucaj A, Mahay K, Oblak M, Gale C, Pye M, McGill Y, Redfearn H, Fearnley M. Management of dyslipidaemia in patients with coronary heart disease: Results from the ESC-EORP EUROASPIRE V survey in 27 countries. Atherosclerosis 2019; 285:135-146. [DOI: 10.1016/j.atherosclerosis.2019.03.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/22/2019] [Accepted: 03/19/2019] [Indexed: 12/16/2022]
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Neumann J, Ziegler K, Gelléri M, Fröhlich-Nowoisky J, Liu F, Bellinghausen I, Schuppan D, Birk U, Pöschl U, Cremer C, Lucas K. Nanoscale distribution of TLR4 on primary human macrophages stimulated with LPS and ATI. Nanoscale 2019; 11:9769-9779. [PMID: 31066732 DOI: 10.1039/c9nr00943d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Toll-like receptor 4 (TLR4) plays a crucial role in the recognition of invading pathogens. Upon activation by lipopolysaccharides (LPS), TLR4 is recruited into specific membrane domains and dimerizes. In addition to LPS, TLR4 can be stimulated by wheat amylase-trypsin inhibitors (ATI). ATI are proteins associated with gluten containing grains, whose ingestion promotes intestinal and extraintestinal inflammation. However, the effect of ATI vs. LPS on the membrane distribution of TLR4 at the nanoscale has not been analyzed. In this study, we investigated the effect of LPS and ATI stimulation on the membrane distribution of TLR4 in primary human macrophages using single molecule localization microscopy (SMLM). We found that in unstimulated macrophages the majority of TLR4 molecules are located in clusters, but with donor-dependent variations from ∼51% to ∼75%. Depending on pre-clustering, we found pronounced variations in the fraction of clustered molecules and density of clusters on the membrane upon LPS and ATI stimulation. Although clustering differed greatly among the human donors, we found an almost constant cluster diameter of ∼44 nm for all donors, independent of treatment. Together, our results show donor-dependent but comparable effects between ATI and LPS stimulation on the membrane distribution of TLR4. This may indicate a general mechanism of TLR4 activation in primary human macrophages. Furthermore, our methodology visualizes TLR4 receptor clustering and underlines its functional role as a signaling platform.
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Affiliation(s)
- Jan Neumann
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128 Mainz, Germany.
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Lee JH, Laure Djikimi Tchetgna F, Krufczik M, Schmitt E, Cremer C, estvater FB, Hausmann M. COMBO-FISH: A Versatile Tool Beyond Standard FISH to Study Chromatin Organization by Fluorescence Light Microscopy. ACTA ACUST UNITED AC 2019. [DOI: 10.21926/obm.genet.1901064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Kordon MM, Szczurek A, Berniak K, Szelest O, Solarczyk K, Tworzydło M, Wachsmann-Hogiu S, Vaahtokari A, Cremer C, Pederson T, Dobrucki JW. PML-like subnuclear bodies, containing XRCC1, juxtaposed to DNA replication-based single-strand breaks. FASEB J 2019; 33:2301-2313. [PMID: 30260704 PMCID: PMC6993927 DOI: 10.1096/fj.201801379r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 07/05/2018] [Accepted: 08/27/2018] [Indexed: 12/14/2022]
Abstract
DNA lesions induce recruitment and accumulation of various repair factors, resulting in formation of discrete nuclear foci. Using superresolution fluorescence microscopy as well as live cell and quantitative imaging, we demonstrate that X-ray repair cross-complementing protein 1 (XRCC1), a key factor in single-strand break and base excision repair, is recruited into nuclear bodies formed in response to replication-related single-strand breaks. Intriguingly, these bodies are assembled immediately in the vicinity of these breaks and never fully colocalize with replication foci. They are structurally organized, containing canonical promyelocytic leukemia (PML) nuclear body protein SP100 concentrated in a peripheral layer, and XRCC1 in the center. They also contain other factors, including PML, poly(ADP-ribose) polymerase 1 (PARP1), ligase IIIα, and origin recognition complex subunit 5. The breast cancer 1 and -2 C terminus domains of XRCC1 are essential for formation of these repair foci. These results reveal that XRCC1-contaning foci constitute newly recognized PML-like nuclear bodies that accrete and locally deliver essential factors for repair of single-strand DNA breaks in replication regions.-Kordon, M. M., Szczurek, A., Berniak, K., Szelest, O., Solarczyk, K., Tworzydło, M., Wachsmann-Hogiu, S., Vaahtokari, A., Cremer, C., Pederson, T., Dobrucki, J. W. PML-like subnuclear bodies, containing XRCC1, juxtaposed to DNA replication-based single-strand breaks.
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Affiliation(s)
- Magdalena M. Kordon
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Aleksander Szczurek
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
- Superresolution Microscopy Group, Institute of Molecular Biology, Mainz, Germany
| | - Krzysztof Berniak
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Oskar Szelest
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Kamil Solarczyk
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Magdalena Tworzydło
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Sebastian Wachsmann-Hogiu
- Department of Pathology and Laboratory Medicine, University of California at Davis, Davis, California, USA
| | - Anne Vaahtokari
- The Francis Crick Institute, Cancer Research UK, London, United Kingdom; and
| | - Christoph Cremer
- Superresolution Microscopy Group, Institute of Molecular Biology, Mainz, Germany
| | - Thoru Pederson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jurek W. Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
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Ziegler K, Neumann J, Liu F, Fröhlich-Nowoisky J, Cremer C, Saloga J, Reinmuth-Selzle K, Pöschl U, Schuppan D, Bellinghausen I, Lucas K. Nitration of Wheat Amylase Trypsin Inhibitors Increases Their Innate and Adaptive Immunostimulatory Potential in vitro. Front Immunol 2019; 9:3174. [PMID: 30740114 PMCID: PMC6357940 DOI: 10.3389/fimmu.2018.03174] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/24/2018] [Indexed: 01/22/2023] Open
Abstract
Amylase trypsin inhibitors (ATI) can be found in all gluten containing cereals and are, therefore, ingredient of basic foods like bread or pasta. In the gut ATI can mediate innate immunity via activation of the Toll-like receptor 4 (TLR4) on immune cells residing in the lamina propria, promoting intestinal, as well as extra-intestinal, inflammation. Inflammatory conditions can induce formation of peroxynitrite (ONOO-) and, thereby, endogenous protein nitration in the body. Moreover, air pollutants like ozone (O3) and nitrogen dioxide (NO2) can cause exogenous protein nitration in the environment. Both reaction pathways may lead to the nitration of ATI. To investigate if and how nitration modulates the immunostimulatory properties of ATI, they were chemically modified by three different methods simulating endogenous and exogenous protein nitration and tested in vitro. Here we show that ATI nitration was achieved by all three methods and lead to increased immune reactions. We found that ATI nitrated by tetranitromethane (TNM) or ONOO- lead to a significantly enhanced TLR4 activation. Furthermore, in human primary immune cells, TNM nitrated ATI induced a significantly higher T cell proliferation and release of Th1 and Th2 cytokines compared to unmodified ATI. Our findings implicate a causative chain between nitration, enhanced TLR4 stimulation, and adaptive immune responses, providing major implications for public health, as nitrated ATI may strongly promote inhalative wheat allergies (baker's asthma), non-celiac wheat sensitivity (NCWS), other allergies, and autoimmune diseases. This underlines the importance of future work analyzing the relationship between endo- and exogenous protein nitration, and the rise in incidence of ATI-related and other food hypersensitivities.
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Affiliation(s)
- Kira Ziegler
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Jan Neumann
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany.,Institute of Molecular Biology, Mainz, Germany
| | - Fobang Liu
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | | | - Christoph Cremer
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany.,Institute of Molecular Biology, Mainz, Germany
| | - Joachim Saloga
- Department of Dermatology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | | | - Ulrich Pöschl
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Detlef Schuppan
- Institute of Translational Immunology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Iris Bellinghausen
- Department of Dermatology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Kurt Lucas
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
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Chen SY, Bestvater F, Schaufler W, Heintzmann R, Cremer C. Patterned illumination single molecule localization microscopy (piSMLM): user defined blinking regions of interest. Opt Express 2018; 26:30009-30020. [PMID: 30469881 DOI: 10.1364/oe.26.030009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/05/2018] [Indexed: 05/23/2023]
Abstract
Single molecule localization microscopy (SMLM) has been established as an important super-resolution technique for studying subcellular structures with a resolution down to a lateral scale of 10 nm. Usually samples are illuminated with a Gaussian shaped beam and consequently insufficient irradiance on the periphery of the illuminated region leads to artifacts in the reconstructed image which degrades image quality. We present a newly developed patterned illumination SMLM (piSMLM) to overcome the problem of uneven illumination by computer-generated holography. By utilizing a phase-only spatial light modulator (SLM) in combination with a modified Gerchberg-Saxton algorithm, a user-defined pattern with homogeneous and nearly speckle-free illumination is obtained. Our experimental results show that irradiance 1 to 5 kW/cm2 was achieved by using a laser with an output power of 200 mW in a region of 2000 µm2 to 500 µm2, respectively. Higher irradiance of up to 20 kW/cm2 can be reached by simply reducing the size of the region of interest (ROI). To demonstrate the application of the piSMLM, nuclear structures were imaged based on fluctuation binding-activated localization microscopy (fBALM). The super-resolution fBALM images revealed nuclear structures at a nanometer scale.
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Schink A, Neumann J, Leifke AL, Ziegler K, Fröhlich-Nowoisky J, Cremer C, Thines E, Weber B, Pöschl U, Schuppan D, Lucas K. Screening of herbal extracts for TLR2- and TLR4-dependent anti-inflammatory effects. PLoS One 2018; 13:e0203907. [PMID: 30307962 PMCID: PMC6181297 DOI: 10.1371/journal.pone.0203907] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/29/2018] [Indexed: 12/18/2022] Open
Abstract
Herbal extracts represent an ample source of natural compounds, with potential to be used in improving human health. There is a growing interest in using natural extracts as possible new treatment strategies for inflammatory diseases. We therefore aimed at identifying herbal extracts that affect inflammatory signaling pathways through toll-like receptors (TLRs), TLR2 and TLR4. Ninety-nine ethanolic extracts were screened in THP-1 monocytes and HeLa-TLR4 transfected reporter cells for their effects on stimulated TLR2 and TLR4 signaling pathways. The 28 identified anti-inflammatory extracts were tested in comparative assays of stimulated HEK-TLR2 and HEK-TLR4 transfected reporter cells to differentiate between direct TLR4 antagonistic effects and interference with downstream signaling cascades. Furthermore, the ten most effective anti-inflammatory extracts were tested on their ability to inhibit nuclear factor-κB (NF-κB) translocation in HeLa-TLR4 transfected reporter cell lines and for their ability to repolarize M1-type macrophages. Ethanolic extracts which showed the highest anti-inflammatory potential, up to a complete inhibition of pro-inflammatory cytokine production were Castanea sativa leaves, Cinchona pubescens bark, Cinnamomum verum bark, Salix alba bark, Rheum palmatum root, Alchemilla vulgaris plant, Humulus lupulus cones, Vaccinium myrtillus berries, Curcuma longa root and Arctostaphylos uva-ursi leaves. Moreover, all tested extracts mitigated not only TLR4, but also TLR2 signaling pathways. Seven of them additionally inhibited translocation of NF-κB into the nucleus. Two of the extracts showed impact on repolarization of pro-inflammatory M1-type to anti-inflammatory M2-type macrophages. Several promising anti-inflammatory herbal extracts were identified in this study, including extracts with previously unknown influence on key TLR signaling pathways and macrophage repolarization, serving as a basis for novel lead compound identification.
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Affiliation(s)
- Anne Schink
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Jan Neumann
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Anna Lena Leifke
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Kira Ziegler
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | | | - Christoph Cremer
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Eckhard Thines
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH, Kaiserslautern, Germany
- Institute of Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Bettina Weber
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Ulrich Pöschl
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Detlef Schuppan
- Institute of Translational Immunology, University of Mainz Medical Center, Mainz, Germany
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States of America
| | - Kurt Lucas
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
- * E-mail:
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Abstract
4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters. Microscopic evidence for this higher order chromatin landscape was strengthened by chromosome conformation capture studies, in particular Hi-C. This approach demonstrated ~1 Mb sized, topologically associating domains in mammalian cell nuclei separated by boundaries. Mutations, which destroy boundaries, can result in developmental disorders and cancer. Nucleosomes appeared first as tetramers in the Archaea kingdom and later evolved to octamers built up each from two H2A, two H2B, two H3, and two H4 proteins. Notably, nucleosomes were lost during the evolution of the Dinoflagellata phylum. Dinoflagellate chromosomes remain condensed during the entire cell cycle, but their chromosome architecture differs radically from the architecture of other eukaryotes. In summary, the conservation of fundamental features of higher order chromatin arrangements throughout the evolution of metazoan animals suggests the existence of conserved, but still unknown mechanism(s) controlling this architecture. Notwithstanding this conservation, a comparison of metazoans and protists also demonstrates species-specific structural and functional features of nuclear organization.
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Affiliation(s)
- T Cremer
- Biocenter, Department of Biology II, Ludwig Maximilian University (LMU), Munich, Germany.
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Hausmann M, Ilić N, Pilarczyk G, Lee JH, Logeswaran A, Borroni AP, Krufczik M, Theda F, Waltrich N, Bestvater F, Hildenbrand G, Cremer C, Blank M. Challenges for Super-Resolution Localization Microscopy and Biomolecular Fluorescent Nano-Probing in Cancer Research. Int J Mol Sci 2017; 18:E2066. [PMID: 28956810 PMCID: PMC5666748 DOI: 10.3390/ijms18102066] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 09/21/2017] [Accepted: 09/23/2017] [Indexed: 11/17/2022] Open
Abstract
Understanding molecular interactions and regulatory mechanisms in tumor initiation, progression, and treatment response are key requirements towards advanced cancer diagnosis and novel treatment procedures in personalized medicine. Beyond decoding the gene expression, malfunctioning and cancer-related epigenetic pathways, investigations of the spatial receptor arrangements in membranes and genome organization in cell nuclei, on the nano-scale, contribute to elucidating complex molecular mechanisms in cells and tissues. By these means, the correlation between cell function and spatial organization of molecules or molecular complexes can be studied, with respect to carcinogenesis, tumor sensitivity or tumor resistance to anticancer therapies, like radiation or antibody treatment. Here, we present several new applications for bio-molecular nano-probes and super-resolution, laser fluorescence localization microscopy and their potential in life sciences, especially in biomedical and cancer research. By means of a tool-box of fluorescent antibodies, green fluorescent protein (GFP) tagging, or specific oligonucleotides, we present tumor relevant re-arrangements of Erb-receptors in membranes, spatial organization of Smad specific ubiquitin protein ligase 2 (Smurf2) in the cytosol, tumor cell characteristic heterochromatin organization, and molecular re-arrangements induced by radiation or antibody treatment. The main purpose of this article is to demonstrate how nano-scaled distance measurements between bio-molecules, tagged by appropriate nano-probes, can be applied to elucidate structures and conformations of molecular complexes which are characteristic of tumorigenesis and treatment responses. These applications open new avenues towards a better interpretation of the spatial organization and treatment responses of functionally relevant molecules, at the single cell level, in normal and cancer cells, offering new potentials for individualized medicine.
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Affiliation(s)
- Michael Hausmann
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Nataša Ilić
- Laboratory of Molecular and Cellular Cancer Biology, Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold ST, Safed 1311502, Israel.
| | - Götz Pilarczyk
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Jin-Ho Lee
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Abiramy Logeswaran
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Aurora Paola Borroni
- Laboratory of Molecular and Cellular Cancer Biology, Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold ST, Safed 1311502, Israel.
| | - Matthias Krufczik
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Franziska Theda
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Nadine Waltrich
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Felix Bestvater
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
- Department of Radiation Oncology, Universitätsmedizin Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 3-5, 68159 Mannheim, Germany.
| | - Christoph Cremer
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.
| | - Michael Blank
- Laboratory of Molecular and Cellular Cancer Biology, Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold ST, Safed 1311502, Israel.
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28
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Szczurek A, Klewes L, Xing J, Gourram A, Birk U, Knecht H, Dobrucki JW, Mai S, Cremer C. Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations. Nucleic Acids Res 2017; 45:e56. [PMID: 28082388 PMCID: PMC5416826 DOI: 10.1093/nar/gkw1301] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 01/10/2017] [Indexed: 01/14/2023] Open
Abstract
Advanced light microscopy is an important tool for nanostructure analysis of chromatin. In this report we present a general concept for Single Molecule localization Microscopy (SMLM) super-resolved imaging of DNA-binding dyes based on modifying the properties of DNA and the dye. By careful adjustment of the chemical environment leading to local, reversible DNA melting and hybridization control over the fluorescence signal of the DNA-binding dye molecules can be introduced. We postulate a transient binding as the basis for our variation of binding-activated localization microscopy (BALM). We demonstrate that several intercalating and minor-groove binding DNA dyes can be used to register (optically isolate) only a few DNA-binding dye signals at a time. To highlight this DNA structure fluctuation-assisted BALM (fBALM), we applied it to measure, for the first time, nanoscale differences in nuclear architecture in model ischemia with an anticipated structural resolution of approximately 50 nm. Our data suggest that this approach may open an avenue for the enhanced microscopic analysis of chromatin nano-architecture and hence the microscopic analysis of nuclear structure aberrations occurring in various pathological conditions. It may also become possible to analyse nuclear nanostructure differences in different cell types, stages of development or environmental stress conditions.
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Affiliation(s)
| | - Ludger Klewes
- University of Manitoba, Cancer Care Manitoba, Winnipeg R3E 0V9, Canada
| | - Jun Xing
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Amine Gourram
- Institute of Molecular Biology, 55128 Mainz, Germany.,Physics Department University Mainz (JGU), 55128 Mainz, Germany
| | - Udo Birk
- Institute of Molecular Biology, 55128 Mainz, Germany.,Physics Department University Mainz (JGU), 55128 Mainz, Germany
| | - Hans Knecht
- Département de Médecine, CHUS, Université de Sherbrooke, 3001-12e Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada.,Department of Medicine, Jewish General Hospital, McGill University, 3755 Côte-Ste-Catherine Road, Montreal, Québec H3T 1E2, Canada
| | - Jurek W Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Sabine Mai
- University of Manitoba, Cancer Care Manitoba, Winnipeg R3E 0V9, Canada
| | - Christoph Cremer
- Institute of Molecular Biology, 55128 Mainz, Germany.,Physics Department University Mainz (JGU), 55128 Mainz, Germany.,Kirchhoff Institute of Physics (KIP), and Institute of Pharmacy & Molecular Biotechnology (IPMB), University Heidelberg, Germany
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Richter V, Bruns S, Bruns T, Weber P, Wagner M, Cremer C, Schneckenburger H. Axial tomography in live cell laser microscopy. J Biomed Opt 2017; 22:91505. [PMID: 28122077 DOI: 10.1117/1.jbo.22.9.091505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/03/2017] [Indexed: 06/06/2023]
Abstract
Single cell microscopy in a three-dimensional (3-D) environment is reported. Cells are grown in an agarose culture gel, located within microcapillaries and observed from different sides after adaptation of an innovative device for sample rotation. Thus, z -stacks can be recorded by confocal microscopy in different directions and used for illustration in 3-D. This gives additional information, since cells or organelles that appear superimposed in one direction, may be well resolved in another one. The method is tested and validated with single cells expressing a membrane or a mitochondrially associated green fluorescent protein, or cells accumulating fluorescent quantum dots. In addition, axial tomography supports measurements of cellular uptake and distribution of the anticancer drug doxorubicin in the nucleus (2 to 6 h after incubation) or the cytoplasm (24 h). This paper discusses that upon cell rotation an enhanced optical resolution in lateral direction compared to axial direction can be utilized to obtain an improved effective 3-D resolution, which represents an important step toward super-resolution microscopy of living cells.
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Affiliation(s)
- Verena Richter
- Aalen University, Institute of Applied Research, Beethovenstraße 1, 73430 Aalen, Germany
| | - Sarah Bruns
- Aalen University, Institute of Applied Research, Beethovenstraße 1, 73430 Aalen, Germany
| | - Thomas Bruns
- Aalen University, Institute of Applied Research, Beethovenstraße 1, 73430 Aalen, Germany
| | - Petra Weber
- Aalen University, Institute of Applied Research, Beethovenstraße 1, 73430 Aalen, Germany
| | - Michael Wagner
- Aalen University, Institute of Applied Research, Beethovenstraße 1, 73430 Aalen, Germany
| | - Christoph Cremer
- University of Heidelberg, Institute of Pharmacy and Molecular Biology, Im Neuenheimer Feld 364, 69120 Heidelberg, GermanycInstitute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
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Bach M, Savini C, Krufczik M, Cremer C, Rösl F, Hausmann M. Super-Resolution Localization Microscopy of γ-H2AX and Heterochromatin after Folate Deficiency. Int J Mol Sci 2017; 18:ijms18081726. [PMID: 28786938 PMCID: PMC5578116 DOI: 10.3390/ijms18081726] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 07/31/2017] [Accepted: 08/04/2017] [Indexed: 01/08/2023] Open
Abstract
Folate is an essential water-soluble vitamin in food and nutrition supplements. As a one-carbon source, it is involved in many central regulatory processes, such as DNA, RNA, and protein methylation as well as DNA synthesis and repair. Deficiency in folate is considered to be associated with an increased incidence of several malignancies, including cervical cancer that is etiologically linked to an infection with “high-risk” human papilloma viruses (HPV). However, it is still not known how a recommended increase in dietary folate after its deprivation affects the physiological status of cells. To study the impact of folate depletion and its subsequent reconstitution in single cells, we used quantitative chromatin conformation measurements obtained by super-resolution fluorescence microscopy, i.e., single molecule localization microscopy (SMLM). As a read-out, we examined the levels and the (re)positioning of γ-H2AX tags and histone H3K9me3 heterochromatin tags after immunostaining in three-dimensional (3D)-conserved cell nuclei. As model, we used HPV16 positive immortalized human keratinocytes that were cultivated under normal, folate deficient, and reconstituted conditions for different periods of time. The results were compared to cells continuously cultivated in standard folate medium. After 13 weeks in low folate, an increase in the phosphorylation of the histone H2AX was noted, indicative of an accumulation of DNA double strand breaks. DNA repair activity represented by the formation of those γ-H2AX clusters was maintained during the following 15 weeks of examination. However, the clustered arrangements of tags appeared to relax in a time-dependent manner. Parallel to the repair activity, the chromatin methylation activity increased as detected by H3K9me3 tags. The progress of DNA double strand repair was accompanied by a reduction of the detected nucleosome density around the γ-H2AX clusters, suggesting a shift from hetero- to euchromatin to allow access to the repair machinery. In conclusion, these data demonstrated a folate-dependent repair activity and chromatin re-organization on the SMLM nanoscale level. This offers new opportunities to further investigate folate-induced chromatin re-organization and the associated mechanisms.
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Affiliation(s)
- Margund Bach
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, Heidelberg 69120, Germany.
| | - Claudia Savini
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
| | - Matthias Krufczik
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, Heidelberg 69120, Germany.
| | - Christoph Cremer
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, Heidelberg 69120, Germany.
- Institute for Molecular Biology, Ackermannweg 4, Mainz 55128, Germany.
| | - Frank Rösl
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, Heidelberg 69120, Germany.
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31
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Birk U, Hase JV, Cremer C. Super-resolution microscopy with very large working distance by means of distributed aperture illumination. Sci Rep 2017; 7:3685. [PMID: 28623362 PMCID: PMC5473833 DOI: 10.1038/s41598-017-03743-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 05/05/2017] [Indexed: 02/03/2023] Open
Abstract
The limits of conventional light microscopy ("Abbe-Limit") depend critically on the numerical aperture (NA) of the objective lens. Imaging at large working distances or a large field-of-view typically requires low NA objectives, thereby reducing the optical resolution to the multi micrometer range. Based on numerical simulations of the intensity field distribution, we present an illumination concept for a super-resolution microscope which allows a three dimensional (3D) optical resolution around 150 nm for working distances up to the centimeter regime. In principle, the system allows great flexibility, because the illumination concept can be used to approximate the point-spread-function of conventional microscope optics, with the additional benefit of a customizable pupil function. Compared with the Abbe-limit using an objective lens with such a large working distance, a volume resolution enhancement potential in the order of 104 is estimated.
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Affiliation(s)
- Udo Birk
- Superresolution Microscopy, Institute of Molecular Biology (IMB), D-55128, Mainz, Germany
- Physics Department University Mainz (JGU), D-55128, Mainz, Germany
- Kirchhoff Institute for Physics, University Heidelberg, D-69120, Heidelberg, Germany
| | - Johann V Hase
- Institute of Pharmacy&Molecular Biotechnology (IPMB), University Heidelberg, D-69120, Heidelberg, Germany
| | - Christoph Cremer
- Superresolution Microscopy, Institute of Molecular Biology (IMB), D-55128, Mainz, Germany.
- Physics Department University Mainz (JGU), D-55128, Mainz, Germany.
- Kirchhoff Institute for Physics, University Heidelberg, D-69120, Heidelberg, Germany.
- Institute of Pharmacy&Molecular Biotechnology (IPMB), University Heidelberg, D-69120, Heidelberg, Germany.
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32
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Cremer C, Szczurek A, Schock F, Gourram A, Birk U. Super-resolution microscopy approaches to nuclear nanostructure imaging. Methods 2017; 123:11-32. [PMID: 28390838 DOI: 10.1016/j.ymeth.2017.03.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/23/2017] [Indexed: 12/14/2022] Open
Abstract
The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has far-reaching functional consequences for gene regulation. Until recently, it appeared to be impossible to study this problem on the nanoscale by light microscopy. However, novel developments in optical imaging technology have radically surpassed the limited resolution of conventional far-field fluorescence microscopy (ca. 200nm). After a brief review of available super-resolution microscopy (SRM) methods, we focus on a specific SRM approach to study nuclear genome structure at the single cell/single molecule level, Spectral Precision Distance/Position Determination Microscopy (SPDM). SPDM, a variant of localization microscopy, makes use of conventional fluorescent proteins or single standard organic fluorophores in combination with standard (or only slightly modified) specimen preparation conditions; in its actual realization mode, the same laser frequency can be used for both photoswitching and fluorescence read out. Presently, the SPDM method allows us to image nuclear genome organization in individual cells down to few tens of nanometer (nm) of structural resolution, and to perform quantitative analyses of individual small chromatin domains; of the nanoscale distribution of histones, chromatin remodeling proteins, and transcription, splicing and repair related factors. As a biomedical research application, using dual-color SPDM, it became possible to monitor in mouse cardiomyocyte cells quantitatively the effects of ischemia conditions on the chromatin nanostructure (DNA). These novel "molecular optics" approaches open an avenue to study the nuclear landscape directly in individual cells down to the single molecule level and thus to test models of functional genome architecture at unprecedented resolution.
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Affiliation(s)
- Christoph Cremer
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany. http://www.optics.imb-mainz.de
| | - Aleksander Szczurek
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Florian Schock
- Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
| | - Amine Gourram
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Udo Birk
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
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33
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Pierzyńska-Mach A, Szczurek A, Cella Zanacchi F, Pennacchietti F, Drukała J, Diaspro A, Cremer C, Darzynkiewicz Z, Dobrucki JW. Subnuclear localization, rates and effectiveness of UVC-induced unscheduled DNA synthesis visualized by fluorescence widefield, confocal and super-resolution microscopy. Cell Cycle 2017; 15:1156-67. [PMID: 27097376 DOI: 10.1080/15384101.2016.1158377] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Unscheduled DNA synthesis (UDS) is the final stage of the process of repair of DNA lesions induced by UVC. We detected UDS using a DNA precursor, 5-ethynyl-2'-deoxyuridine (EdU). Using wide-field, confocal and super-resolution fluorescence microscopy and normal human fibroblasts, derived from healthy subjects, we demonstrate that the sub-nuclear pattern of UDS detected via incorporation of EdU is different from that when BrdU is used as DNA precursor. EdU incorporation occurs evenly throughout chromatin, as opposed to just a few small and large repair foci detected by BrdU. We attribute this difference to the fact that BrdU antibody is of much larger size than EdU, and its accessibility to the incorporated precursor requires the presence of denatured sections of DNA. It appears that under the standard conditions of immunocytochemical detection of BrdU only fragments of DNA of various length are being denatured. We argue that, compared with BrdU, the UDS pattern visualized by EdU constitutes a more faithful representation of sub-nuclear distribution of the final stage of nucleotide excision repair induced by UVC. Using the optimized integrated EdU detection procedure we also measured the relative amount of the DNA precursor incorporated by cells during UDS following exposure to various doses of UVC. Also described is the high degree of heterogeneity in terms of the UVC-induced EdU incorporation per cell, presumably reflecting various DNA repair efficiencies or differences in the level of endogenous dT competing with EdU within a population of normal human fibroblasts.
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Affiliation(s)
- Agnieszka Pierzyńska-Mach
- a Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Kraków , Poland
| | | | | | | | - Justyna Drukała
- d Department of Cell Biology , Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Kraków , Poland
| | - Alberto Diaspro
- c Nanoscopy, Istituto Italiano di Tecnologia , Genova , Italy
| | | | - Zbigniew Darzynkiewicz
- e Brander Cancer Research Institute and Department of Pathology, New York Medical College , Valhalla , NY , USA
| | - Jurek W Dobrucki
- a Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Kraków , Poland
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Boyd PS, Struve N, Bach M, Eberle JP, Gote M, Schock F, Cremer C, Kriegs M, Hausmann M. Clustered localization of EGFRvIII in glioblastoma cells as detected by high precision localization microscopy. Nanoscale 2016; 8:20037-20047. [PMID: 27883139 DOI: 10.1039/c6nr05880a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
For receptor tyrosine kinases supramolecular organization on the cell membrane is critical for their function. Super-resolution fluorescence microscopy techniques have offered new opportunities for the analysis of single receptor localization. Here, we analysed the cluster formation of the epidermal growth factor receptor variant III (EGFRvIII), a deletion variant which is expressed in glioblastoma. The constitutively activated variant EGFRvIII is expressed in cells with an egfr gene amplification and is thought to enhance the tumorigenic potential especially of glioblastoma cells. Due to the lack of an adequate model system, it is still unclear how endogenous EGFRvIII expression alters cellular signalling and if it is organized in clusters like the wild type receptor. We have recently described the establishment of two pairs of iso-genetic cell lines (BS153 and DKMG), displaying endogenous EGFRvIII expression or not. Using these cell lines we investigated single receptor localization of EGFRvIII by high precision localization microscopy. Cluster analysis revealed that EGFRvIII is present in clusters on the surface of the cells, with about 60% or even more receptor molecules being assembled in clusters of approximately 100 nm in diameter whereby the cluster definition was iteratively determined. The signal to signal distance may indicate dimer formation while signal quantification indicates 1 × 106-5 × 106 EGFRvIII molecules per cell. Altogether, these data give unique insights into the membrane surface localization of EGFRvIII in glioblastoma cells. These insights will help to unveil the function of this tumour associated receptor variant which might lead to a better understanding of glioblastoma and therefore could lead to improved therapy approaches.
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Affiliation(s)
- Philip S Boyd
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
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35
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Oleksiuk O, Abba M, Tezcan KC, Schaufler W, Bestvater F, Patil N, Birk U, Hafner M, Altevogt P, Cremer C, Allgayer H. Single-Molecule Localization Microscopy allows for the analysis of cancer metastasis-specific miRNA distribution on the nanoscale. Oncotarget 2016; 6:44745-57. [PMID: 26561203 PMCID: PMC4792589 DOI: 10.18632/oncotarget.6297] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 10/23/2015] [Indexed: 01/03/2023] Open
Abstract
We describe a novel approach for the detection of small non-coding RNAs in single cells by Single-Molecule Localization Microscopy (SMLM). We used a modified SMLM–setup and applied this instrument in a first proof-of-principle concept to human cancer cell lines. Our method is able to visualize single microRNA (miR)-molecules in fixed cells with a localization accuracy of 10–15 nm, and is able to quantify and analyse clustering and localization in particular subcellular sites, including exosomes. We compared the metastasis-site derived (SW620) and primary site derived (SW480) human colorectal cancer (CRC) cell lines, and (as a proof of principle) evaluated the metastasis relevant miR-31 as a first example. We observed that the subcellular distribution of miR-31 molecules in both cell lines was very heterogeneous with the largest subpopulation of optically acquired weakly metastatic cells characterized by a low number of miR-31 molecules, as opposed to a significantly higher number in the majority of the highly metastatic cells. Furthermore, the highly metastatic cells had significantly more miR-31-molecules in the extracellular space, which were visualized to co-localize with exosomes in significantly higher numbers. From this study, we conclude that miRs are not only aberrantly expressed and regulated, but also differentially compartmentalized in cells with different metastatic potential. Taken together, this novel approach, by providing single molecule images of miRNAs in cellulo can be used as a powerful supplementary tool in the analysis of miRNA function and behaviour and has far reaching potential in defining metastasis-critical subpopulations within a given heterogeneous cancer cell population.
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Affiliation(s)
- Olga Oleksiuk
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.,Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Mohammed Abba
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.,Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Kerem Can Tezcan
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.,Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Wladimir Schaufler
- Light Microscopy Facility, German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Karlsruhe Institute of Technology, Karlsruhe University, Karlsruhe, Germany
| | - Felix Bestvater
- Light Microscopy Facility, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Nitin Patil
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.,Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Udo Birk
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Mathias Hafner
- Institute for Molecular and Cellular Biology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Peter Altevogt
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg and Dept. of Dermatology, Venereology and Allergology, UMM, University of Heidelberg, Heidelberg, Germany
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Mainz, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg, Germany
| | - Heike Allgayer
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.,Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Heidelberg, Germany
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36
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Szczurek A, Xing J, Birk UJ, Cremer C. Single Molecule Localization Microscopy of Mammalian Cell Nuclei on the Nanoscale. Front Genet 2016; 7:114. [PMID: 27446198 PMCID: PMC4919319 DOI: 10.3389/fgene.2016.00114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/02/2016] [Indexed: 11/13/2022] Open
Abstract
Nuclear texture analysis is a well-established method of cellular pathology. It is hampered, however, by the limits of conventional light microscopy (ca. 200 nm). These limits have been overcome by a variety of super-resolution approaches. An especially promising approach to chromatin texture analysis is single molecule localization microscopy (SMLM) as it provides the highest resolution using fluorescent based methods. At the present state of the art, using fixed whole cell samples and standard DNA dyes, a structural resolution of chromatin in the 50–100 nm range is obtained using SMLM. We highlight how the combination of localization microscopy with standard fluorophores opens the avenue to a plethora of studies including the spatial distribution of DNA and associated proteins in eukaryotic cell nuclei with the potential to elucidate the functional organization of chromatin. These views are based on our experience as well as on recently published research in this field.
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Affiliation(s)
| | - Jun Xing
- Superresolution Microscopy, Institute of Molecular Biology Mainz, Germany
| | - Udo J Birk
- Superresolution Microscopy, Institute of Molecular BiologyMainz, Germany; Department of Physics, University of MainzMainz, Germany; Department of Physics, University of MainzMainz, Germany
| | - Christoph Cremer
- Superresolution Microscopy, Institute of Molecular BiologyMainz, Germany; Department of Physics, University of MainzMainz, Germany; Kirchhoff Institute of Physics, University of HeidelbergHeidelberg, Germany; Institute of Pharmacy and Molecular Biotechnology, University of HeidelbergHeidelberg, Germany
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Lopez Perez R, Best G, Nicolay NH, Greubel C, Rossberger S, Reindl J, Dollinger G, Weber KJ, Cremer C, Huber PE. Superresolution light microscopy shows nanostructure of carbon ion radiation-induced DNA double-strand break repair foci. FASEB J 2016; 30:2767-76. [PMID: 27166088 DOI: 10.1096/fj.201500106r] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 04/12/2016] [Indexed: 12/13/2022]
Abstract
Carbon ion radiation is a promising new form of radiotherapy for cancer, but the central question about the biologic effects of charged particle radiation is yet incompletely understood. Key to this question is the understanding of the interaction of ions with DNA in the cell's nucleus. Induction and repair of DNA lesions including double-strand breaks (DSBs) are decisive for the cell. Several DSB repair markers have been used to investigate these processes microscopically, but the limited resolution of conventional microscopy is insufficient to provide structural insights. We have applied superresolution microscopy to overcome these limitations and analyze the fine structure of DSB repair foci. We found that the conventionally detected foci of the widely used DSB marker γH2AX (Ø 700-1000 nm) were composed of elongated subfoci with a size of ∼100 nm consisting of even smaller subfocus elements (Ø 40-60 nm). The structural organization of the subfoci suggests that they could represent the local chromatin structure of elementary DSB repair units at the DSB damage sites. Subfocus clusters may indicate induction of densely spaced DSBs, which are thought to be associated with the high biologic effectiveness of carbon ions. Superresolution microscopy might emerge as a powerful tool to improve our knowledge of interactions of ionizing radiation with cells.-Lopez Perez, R., Best, G., Nicolay, N. H., Greubel, C., Rossberger, S., Reindl, J., Dollinger, G., Weber, K.-J., Cremer, C., Huber, P. E. Superresolution light microscopy shows nanostructure of carbon ion radiation-induced DNA double-strand break repair foci.
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Affiliation(s)
- Ramon Lopez Perez
- Clinical Cooperation Unit and Molecular Radiation Oncology, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany;
| | - Gerrit Best
- Department of Ophthalmology, Heidelberg University Hospital, Heidelberg, Germany; Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany
| | - Nils H Nicolay
- Clinical Cooperation Unit and Molecular Radiation Oncology, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christoph Greubel
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany; and
| | - Sabrina Rossberger
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany
| | - Judith Reindl
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany; and
| | - Günther Dollinger
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany; and
| | - Klaus-Josef Weber
- Clinical Cooperation Unit and Molecular Radiation Oncology, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christoph Cremer
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany; Superresolution Microscopy of Functional Nuclear Nanostructure, Institute of Molecular Biology, Mainz, Germany
| | - Peter E Huber
- Clinical Cooperation Unit and Molecular Radiation Oncology, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany;
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Żurek-Biesiada D, Szczurek AT, Prakash K, Mohana GK, Lee HK, Roignant JY, Birk UJ, Dobrucki JW, Cremer C. Localization microscopy of DNA in situ using Vybrant ® DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution. Exp Cell Res 2016; 343:97-106. [DOI: 10.1016/j.yexcr.2015.08.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/27/2015] [Accepted: 08/30/2015] [Indexed: 12/17/2022]
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Moser F, Hildenbrand G, Müller P, Al Saroori A, Biswas A, Bach M, Wenz F, Cremer C, Burger N, Veldwijk MR, Hausmann M. Cellular Uptake of Gold Nanoparticles and Their Behavior as Labels for Localization Microscopy. Biophys J 2016; 110:947-53. [PMID: 26910431 PMCID: PMC4776034 DOI: 10.1016/j.bpj.2016.01.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/21/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022] Open
Abstract
Gold nanoparticles (GNPs) enhance the damaging absorbance effects of high-energy photons in radiation therapy by increasing the emission of Auger-photoelectrons in the nm-μm range. It has been shown that the incorporation of GNPs has a significant effect on radiosensitivity of cells and their dose-dependent clonogenic survival. One major characteristic of GNPs is also their diameter-dependent cellular uptake and retention. In this article, we show by means of an established embodiment of localization microscopy, spectral position determination microscopy (SPDM), that imaging with nanometer resolution and systematic counting of GNPs becomes feasible, because optical absorption and plasmon resonance effects result in optical blinking of GNPs at a size-dependent wavelength. To quantify cellular uptake and retention or release, SPDM with GNPs that have diameters of 10 and 25 nm was performed after 2 h and after 18 h. The uptake of the GNPs in HeLa cells was either achieved via incubation or transfection via DNA labeling. On average, the uptake by incubation after 2 h was approximately double for 10 nm GNPs as compared to 25 nm GNPs. In contrast, the uptake of 25 nm GNPs by transfection was approximately four times higher after 2 h. The spectral characteristics of the fluorescence of the GNPs seem to be environment-dependent. In contrast to fluorescent dyes that show blinking characteristics due to reversible photobleaching, the blinking of GNPs seems to be stable for long periods of time, and this facilitates their use as an appropriate dye analog for SPDM imaging.
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Affiliation(s)
- Felipe Moser
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim; Department of Radiation Oncology, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Patrick Müller
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Alexander Al Saroori
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Abin Biswas
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim; Department of Radiation Oncology, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Margund Bach
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Frederik Wenz
- Department of Radiation Oncology, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Christoph Cremer
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany; Institute of Molecular Biology, Mainz, Germany
| | - Nina Burger
- Department of Radiation Oncology, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Marlon R Veldwijk
- Department of Radiation Oncology, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim.
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Żurek-Biesiada D, Szczurek AT, Prakash K, Best G, Mohana GK, Lee HK, Roignant JY, Dobrucki JW, Cremer C, Birk U. Quantitative super-resolution localization microscopy of DNA in situ using Vybrant® DyeCycle™ Violet fluorescent probe. Data Brief 2016; 7:157-71. [PMID: 27054149 PMCID: PMC4802433 DOI: 10.1016/j.dib.2016.01.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 01/07/2016] [Accepted: 01/20/2016] [Indexed: 02/02/2023] Open
Abstract
Single Molecule Localization Microscopy (SMLM) is a recently emerged optical imaging method that was shown to achieve a resolution in the order of tens of nanometers in intact cells. Novel high resolution imaging methods might be crucial for understanding of how the chromatin, a complex of DNA and proteins, is arranged in the eukaryotic cell nucleus. Such an approach utilizing switching of a fluorescent, DNA-binding dye Vybrant® DyeCycle™ Violet has been previously demonstrated by us (Żurek-Biesiada et al., 2015) [1]. Here we provide quantitative information on the influence of the chemical environment on the behavior of the dye, discuss the variability in the DNA-associated signal density, and demonstrate direct proof of enhanced structural resolution. Furthermore, we compare different visualization approaches. Finally, we describe various opportunities of multicolor DNA/SMLM imaging in eukaryotic cell nuclei.
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Affiliation(s)
- Dominika Żurek-Biesiada
- Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | | | - Kirti Prakash
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Gerrit Best
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
| | - Giriram K Mohana
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Hyun-Keun Lee
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz, Germany
| | - Jean-Yves Roignant
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Jurek W Dobrucki
- Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany; Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany; Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz, Germany
| | - Udo Birk
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany; Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany; Department of Physics, University of Mainz (JGU), Staudingerweg 7, 55128 Mainz, Germany
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Stuhlmüller M, Schwarz-Finsterle J, Fey E, Lux J, Bach M, Cremer C, Hinderhofer K, Hausmann M, Hildenbrand G. In situ optical sequencing and structure analysis of a trinucleotide repeat genome region by localization microscopy after specific COMBO-FISH nano-probing. Nanoscale 2015; 7:17938-17946. [PMID: 26463479 DOI: 10.1039/c5nr04141d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Trinucleotide repeat expansions (like (CGG)n) of chromatin in the genome of cell nuclei can cause neurological disorders such as for example the Fragile-X syndrome. Until now the mechanisms are not clearly understood as to how these expansions develop during cell proliferation. Therefore in situ investigations of chromatin structures on the nanoscale are required to better understand supra-molecular mechanisms on the single cell level. By super-resolution localization microscopy (Spectral Position Determination Microscopy; SPDM) in combination with nano-probing using COMBO-FISH (COMBinatorial Oligonucleotide FISH), novel insights into the nano-architecture of the genome will become possible. The native spatial structure of trinucleotide repeat expansion genome regions was analysed and optical sequencing of repetitive units was performed within 3D-conserved nuclei using SPDM after COMBO-FISH. We analysed a (CGG)n-expansion region inside the 5' untranslated region of the FMR1 gene. The number of CGG repeats for a full mutation causing the Fragile-X syndrome was found and also verified by Southern blot. The FMR1 promotor region was similarly condensed like a centromeric region whereas the arrangement of the probes labelling the expansion region seemed to indicate a loop-like nano-structure. These results for the first time demonstrate that in situ chromatin structure measurements on the nanoscale are feasible. Due to further methodological progress it will become possible to estimate the state of trinucleotide repeat mutations in detail and to determine the associated chromatin strand structural changes on the single cell level. In general, the application of the described approach to any genome region will lead to new insights into genome nano-architecture and open new avenues for understanding mechanisms and their relevance in the development of heredity diseases.
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Affiliation(s)
- M Stuhlmüller
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
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Kirmes I, Szczurek A, Prakash K, Charapitsa I, Heiser C, Musheev M, Schock F, Fornalczyk K, Ma D, Birk U, Cremer C, Reid G. A transient ischemic environment induces reversible compaction of chromatin. Genome Biol 2015; 16:246. [PMID: 26541514 PMCID: PMC4635527 DOI: 10.1186/s13059-015-0802-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022] Open
Abstract
Background Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investigated using single molecule localization microscopy of DNA binding dyes and of acetylated histones, by the sensitivity of chromatin to digestion with DNAseI, and by fluorescence recovery after photobleaching (FRAP) of core and linker histones. Results Short-term oxygen and nutrient deprivation of the cardiomyocyte cell line HL-1 induces a previously undescribed chromatin architecture, consisting of large, chromatin-sparse voids interspersed between DNA-dense hollow helicoid structures 40–700 nm in dimension. The chromatin compaction is reversible, and upon restitution of normoxia and nutrients, chromatin transiently adopts a more open structure than in untreated cells. The compacted state of chromatin reduces transcription, while the open chromatin structure induced upon recovery provokes a transitory increase in transcription. Digestion of chromatin with DNAseI confirms that oxygen and nutrient deprivation induces compaction of chromatin. Chromatin compaction is associated with depletion of ATP and redistribution of the polyamine pool into the nucleus. FRAP demonstrates that core histones are not displaced from compacted chromatin; however, the mobility of linker histone H1 is considerably reduced, to an extent that far exceeds the difference in histone H1 mobility between heterochromatin and euchromatin. Conclusions These studies exemplify the dynamic capacity of chromatin architecture to physically respond to environmental conditions, directly link cellular energy status to chromatin compaction and provide insight into the effect ischemia has on the nuclear architecture of cells. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0802-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ina Kirmes
- Institute for Molecular Biology, 55128, Mainz, Germany
| | | | - Kirti Prakash
- Institute for Molecular Biology, 55128, Mainz, Germany.,Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120, Heidelberg, Germany
| | | | | | | | | | - Karolina Fornalczyk
- Institute for Molecular Biology, 55128, Mainz, Germany.,Department of Molecular Biophysics, University of Łódź, Łódź, Poland
| | - Dongyu Ma
- Institute for Molecular Biology, 55128, Mainz, Germany.,Centre for Biomedicine and Medical Technology Mannheim (CBTM), University of Heidelberg, 68167, Mannheim, Germany
| | - Udo Birk
- Institute for Molecular Biology, 55128, Mainz, Germany
| | - Christoph Cremer
- Institute for Molecular Biology, 55128, Mainz, Germany. .,Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120, Heidelberg, Germany.
| | - George Reid
- Institute for Molecular Biology, 55128, Mainz, Germany.
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Perez RL, Nicolay N, Best G, Cremer C, Huber P. Super-resolution Microscopy Reveals Fine Structure of Carbon Ion Induced DSB Repair Foci in Glioblastoma Cells. Int J Radiat Oncol Biol Phys 2015. [DOI: 10.1016/j.ijrobp.2015.07.1895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Abba M, Oleksiuk O, Tezcan K, Schaufler W, Bestvater F, Altevogt P, Hafner M, Cremer C, Allgayer H. Abstract 204: Single-molecule localization microscopy analysis of a cancer metastasis-specific miRNA on the nanoscale. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-204] [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: 11/16/2022]
Abstract
Abstract
We propose a novel approach for the detection of small non-coding RNAs in cells by Single Molecule Localization Microscopy (SMLM). We describe a modified and upgraded SMLM-setup and apply this instrument in a first proof-of-principle concept to human cancer cell lines. Our method is able to visualize single microRNA molecules in fixed cells with a localization accuracy of 10-15 nm, is able to quantify numbers and analyse clustering and localization in particular subcellular sites, including exosomes. We compared metastatic-site derived and primary site derived human adenocarcinoma cultured colorectal cancer (CRC) cells, and (as a proof of principle) evaluated the metastatically relevant miR-31 as a first example. We observed that the subcellular distribution of miR-31 molecules in all cell lines was very heterogeneous with the largest subpopulation of optically acquired low-metastatic cells characterized by a low number of miR-31 molecules, as opposed to a significantly higher number in the majority of the highly metastatic cells.
Citation Format: Mohammed Abba, Olga Oleksiuk, Kerem Tezcan, Wladimir Schaufler, Felix Bestvater, Peter Altevogt, Mathias Hafner, Christoph Cremer, Heike Allgayer. Single-molecule localization microscopy analysis of a cancer metastasis-specific miRNA on the nanoscale. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 204. doi:10.1158/1538-7445.AM2015-204
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Affiliation(s)
| | | | - Kerem Tezcan
- 1German Cancer Research Ctr., Heidelberg, Germany
| | | | | | | | - Mathias Hafner
- 2Mannheim University of Applied Sciences, Mannheim, Germany
| | | | - Heike Allgayer
- 4Medical Faculty Mannheim, University of Heidelberg and German Cancer Research Ctr., Mannheim, Germany
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Cremer T, Cremer M, Hübner B, Strickfaden H, Smeets D, Popken J, Sterr M, Markaki Y, Rippe K, Cremer C. The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments. FEBS Lett 2015; 589:2931-43. [PMID: 26028501 DOI: 10.1016/j.febslet.2015.05.037] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 02/04/2023]
Abstract
Recent methodological advancements in microscopy and DNA sequencing-based methods provide unprecedented new insights into the spatio-temporal relationships between chromatin and nuclear machineries. We discuss a model of the underlying functional nuclear organization derived mostly from electron and super-resolved fluorescence microscopy studies. It is based on two spatially co-aligned, active and inactive nuclear compartments (ANC and INC). The INC comprises the compact, transcriptionally inactive core of chromatin domain clusters (CDCs). The ANC is formed by the transcriptionally active periphery of CDCs, called the perichromatin region (PR), and the interchromatin compartment (IC). The IC is connected to nuclear pores and serves nuclear import and export functions. The ANC is the major site of RNA synthesis. It is highly enriched in epigenetic marks for transcriptionally competent chromatin and RNA Polymerase II. Marks for silent chromatin are enriched in the INC. Multi-scale cross-correlation spectroscopy suggests that nuclear architecture resembles a random obstacle network for diffusing proteins. An increased dwell time of proteins and protein complexes within the ANC may help to limit genome scanning by factors or factor complexes to DNA exposed within the ANC.
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Affiliation(s)
- Thomas Cremer
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany.
| | - Marion Cremer
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Barbara Hübner
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Hilmar Strickfaden
- University of Alberta, Cross Cancer Institute Dept. of Oncology, Edmonton, AB, Canada
| | - Daniel Smeets
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Jens Popken
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Michael Sterr
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Yolanda Markaki
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) & BioQuant Center, Research Group Genome Organization & Function, Heidelberg, Germany.
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Mainz and Institute of Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Germany.
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Szczurek AT, Prakash K, Lee HK, Żurek-Biesiada DJ, Best G, Hagmann M, Dobrucki JW, Cremer C, Birk U. Single molecule localization microscopy of the distribution of chromatin using Hoechst and DAPI fluorescent probes. Nucleus 2014; 5:331-40. [PMID: 25482122 PMCID: PMC4152347 DOI: 10.4161/nucl.29564] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/06/2014] [Accepted: 06/12/2014] [Indexed: 12/12/2022] Open
Abstract
Several approaches have been described to fluorescently label and image DNA and chromatin in situ on the single-molecule level. These superresolution microscopy techniques are based on detecting optically isolated, fluorescently tagged anti-histone antibodies, fluorescently labeled DNA precursor analogs, or fluorescent dyes bound to DNA. Presently they suffer from various drawbacks such as low labeling efficiency or interference with DNA structure. In this report, we demonstrate that DNA minor groove binding dyes, such as Hoechst 33258, Hoechst 33342, and DAPI, can be effectively employed in single molecule localization microscopy (SMLM) with high optical and structural resolution. Upon illumination with low intensity 405 nm light, a small subpopulation of these molecules stochastically undergoes photoconversion from the original blue-emitting form to a green-emitting form. Using a 491 nm laser excitation, fluorescence of these green-emitting, optically isolated molecules was registered until "bleached". This procedure facilitated substantially the optical isolation and localization of large numbers of individual dye molecules bound to DNA in situ, in nuclei of fixed mammalian cells, or in mitotic chromosomes, and enabled the reconstruction of high-quality DNA density maps. We anticipate that this approach will provide new insights into DNA replication, DNA repair, gene transcription, and other nuclear processes.
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Affiliation(s)
| | - Kirti Prakash
- Institute of Molecular Biology; Mainz, Germany
- Institute for Pharmacy and Molecular Biotechnology; University of Heidelberg; Heidelberg, Germany
| | - Hyun-Keun Lee
- Institute of Molecular Biology; Mainz, Germany
- Department of Physics; University of Mainz; Mainz, Germany
| | | | - Gerrit Best
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
- University Hospital Heidelberg; University of Heidelberg; Heidelberg, Germany
| | - Martin Hagmann
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
- University Hospital Heidelberg; University of Heidelberg; Heidelberg, Germany
| | - Jurek W Dobrucki
- Faculty of Biochemistry, Biophysics, and Biotechnology; Jagiellonian University; Kraków, Poland
| | - Christoph Cremer
- Institute of Molecular Biology; Mainz, Germany
- Institute for Pharmacy and Molecular Biotechnology; University of Heidelberg; Heidelberg, Germany
- Department of Physics; University of Mainz; Mainz, Germany
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
| | - Udo Birk
- Institute of Molecular Biology; Mainz, Germany
- Department of Physics; University of Mainz; Mainz, Germany
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
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Cremer T, Cremer C, Lichter P. Recollections of a scientific journey published in human genetics: from chromosome territories to interphase cytogenetics and comparative genome hybridization. Hum Genet 2014; 133:403-16. [PMID: 24504674 DOI: 10.1007/s00439-014-1425-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 01/19/2014] [Indexed: 10/25/2022]
Abstract
In line with the intentions of an issue celebrating the 50th anniversary of Human Genetics, we focus on a series of frequently cited studies published in this journal during the 1980s and 1990s. These studies have contributed to the rise of molecular cytogenetics. They yielded evidence that chromosomes occupy distinct territories in the mammalian cell nucleus, first obtained with laser-UV-microbeam experiments and thereafter with chromosome painting, and contributed to the development of interphase cytogenetics and comparative genome hybridization. We provide a personal account of experimental concepts, which were developed by us and others, and describe some of the unforeseeable turns and obstacles, which we had to overcome on the way towards an experimental realization. We conclude with a perspective on current developments and goals of molecular cytogenetics.
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Affiliation(s)
- Thomas Cremer
- LMU Biozentrum, Grosshadernerstr. 2, Martinsried, Germany,
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Kaeberich A, Cremer C, Reindl I, Domenger C, Kaiser J, Hauroeder B, Werdan K, Schlitt A. Otamixaban versus UFH, enoxaparin and fondaparinux in the prevention of cardiac catheter thrombosis in vitro (electron microscopic results from the OPEN-CATH study). Eur Heart J 2013. [DOI: 10.1093/eurheartj/eht310.p4851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Rossberger S, Ach T, Best G, Cremer C, Heintzmann R, Dithmar S. High-resolution imaging of autofluorescent particles within drusen using structured illumination microscopy. Br J Ophthalmol 2013; 97:518-23. [PMID: 23410731 DOI: 10.1136/bjophthalmol-2012-302350] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
PURPOSE Autofluorescent (AF) material within drusen has rarely been described and there is little knowledge about origin and formation of these particles. Drusen formation is still a relatively unknown process and analysis of AF inclusions might be important for the understanding of fundamental processes. Here we present a detailed analysis of drusen containing AF material using structured illumination microscopy (SIM), which provides a lateral resolution twice as high as conventional fluorescence microscopy. METHODS Eight histological retinal pigment epithelium (RPE) sections obtained from eight human donor eyes (76 ± 4 years) were examined by SIM using laser light of different wavelengths (488 nm, 568 nm). Drusen were studied with regards to their size and shape. AF material within drusen was analysed in terms of size, shape, AF behaviour, and distribution across drusen. RESULTS A total of 441 drusen were found, of which 101 contained AF material (22.9%). 90.1% of these drusen were smaller than 63 µm (mean: 35.65 µm ± 2.38 µm) regardless of whether classified as hard or soft drusen. AF particles (n=190) within drusen show similar spectra compared with lipofuscin granules in RPE cells. Up to 11 particles were found within a single druse. Nearly all particles were located in the outer 2/3 of the drusen (85.94%). CONCLUSIONS SIM allows studying AF particles within drusen on a higher resolution level compared with conventional fluorescence, multiphoton or even confocal microscopy and therefore provides detailed insights in drusen. Shape and autofluorescence analysis of the material embedded in drusen suggest that these particles originate from the overlaying RPE cells.
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Affiliation(s)
- Sabrina Rossberger
- Department of Ophthalmology, University of Heidelberg, Heidelberg, Germany
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Huber O, Brunner A, Maier P, Kaufmann R, Couraud PO, Cremer C, Fricker G. Localization microscopy (SPDM) reveals clustered formations of P-glycoprotein in a human blood-brain barrier model. PLoS One 2012; 7:e44776. [PMID: 22984556 PMCID: PMC3440331 DOI: 10.1371/journal.pone.0044776] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 08/07/2012] [Indexed: 11/24/2022] Open
Abstract
P-glycoprotein (Pgp; also known as MDR1, ABCB1) is the most important and best studied efflux transporter at the blood-brain barrier (BBB); however, the organization of Pgp is unknown. The aim of this study was to employ the recently developed super-resolution fluorescence microscopy method spectral precision distance microscopy/spectral position determination microscopy (SPDM) to investigate the spatial distribution of Pgp in the luminal plasma membrane of brain capillary endothelial cells. Potential disturbing effects of cell membrane curvatures on the distribution analysis are addressed with computer simulations. Immortalized human cerebral microvascular endothelial cells (hCMEC/D3) served as a model of human BBB. hCMEC/D3 cells were transduced with a Pgp-green fluorescent protein (GFP) fusion protein incorporated in a lentivirus-derived vector. The expression and localization of the Pgp-GFP fusion protein was visualized by SPDM. The limited resolution of SPDM in the z-direction leads to a projection during the imaging process affecting the appeared spatial distribution of fluorescence molecules in the super-resolution images. Therefore, simulations of molecule distributions on differently curved cell membranes were performed and their projected spatial distribution was investigated. Function of the fusion protein was confirmed by FACS analysis after incubation of cells with the fluorescent probe eFluxx-ID Gold in absence and presence of verapamil. More than 112,000 single Pgp-GFP molecules (corresponding to approximately 5,600 Pgp-GFP molecules per cell) were detected by SPDM with an averaged spatial resolution of approximately 40 nm in hCMEC/D3 cells. We found that Pgp-GFP is distributed in clustered formations in hCMEC/D3 cells while the influence of present random cell membrane curvatures can be excluded based on the simulation results. Individual formations are distributed randomly over the cell membrane.
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Affiliation(s)
- Olga Huber
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Alexander Brunner
- Kirchhoff-Institute for Physics, University of Heidelberg, Heidelberg, Germany
- Department of Medical Physics in Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Maier
- Department of Radiation Oncology, Mannheim Medical Centre, University of Heidelberg, Mannheim, Germany
| | - Rainer Kaufmann
- Kirchhoff-Institute for Physics, University of Heidelberg, Heidelberg, Germany
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Christoph Cremer
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
- Kirchhoff-Institute for Physics, University of Heidelberg, Heidelberg, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Gert Fricker
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
- * E-mail:
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