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Greitens C, Leroux JC, Burger M. The intracellular visualization of exogenous DNA in fluorescence microscopy. Drug Deliv Transl Res 2024; 14:2242-2261. [PMID: 38526634 PMCID: PMC11208204 DOI: 10.1007/s13346-024-01563-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 03/27/2024]
Abstract
In the development of non-viral gene delivery vectors, it is essential to reliably localize and quantify transfected DNA inside the cell. To track DNA, fluorescence microscopy methods are commonly applied. These mostly rely on fluorescently labeled DNA, DNA binding proteins fused to a fluorescent protein, or fluorescence in situ hybridization (FISH). In addition, co-stainings are often used to determine the colocalization of the DNA in specific cellular compartments, such as the endolysosomes or the nucleus. We provide an overview of these DNA tracking methods, advice on how they should be combined, and indicate which co-stainings or additional methods are required to draw precise conclusions from a DNA tracking experiment. Some emphasis is given to the localization of exogenous DNA inside the nucleus, which is the last step of DNA delivery. We argue that suitable tools which allow for the nuclear detection of faint signals are still missing, hampering the rational development of more efficient non-viral transfection systems.
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Affiliation(s)
- Christina Greitens
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Jean-Christophe Leroux
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland.
| | - Michael Burger
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland.
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Uryu K, Soplop N, Sheahan TP, Catanese MT, Huynh C, Pena J, Boudreau N, Matei I, Kenific C, Hashimoto A, Hoshino A, Rice CM, Lyden D. Advancement in Cellular Topographic and Nanoparticle Capture Imaging by High Resolution Microscopy Incorporating a Freeze-Drying and Gaseous Nitrogen-based Approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.559906. [PMID: 37808646 PMCID: PMC10557753 DOI: 10.1101/2023.09.28.559906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Scanning electron microscopy (SEM) offers an unparalleled view of the membrane topography of mammalian cells by using a conventional osmium (OsO4) and ethanol-based tissue preparation. However, conventional SEM methods limit optimal resolution due to ethanol and lipid interactions and interfere with visualization of fluorescent reporter proteins. Therefore, SEM correlative light and electron microscopy (CLEM) has been hindered by the adverse effects of ethanol and OsO4 on retention of fluorescence signals. To overcome this technological gap in achieving high-resolution SEM and retain fluorescent reporter signals, we developed a freeze-drying method with gaseous nitrogen (FDGN). We demonstrate that FDGN preserves cyto-architecture to allow visualization of detailed membrane topography while retaining fluorescent signals and that FDGN processing can be used in conjunction with a variety of high-resolution imaging systems to enable collection and validation of unique, high-quality data from these approaches. In particular, we show that FDGN coupled with high resolution microscopy provided detailed insight into viral or tumor-derived extracellular vesicle (TEV)-host cell interactions and may aid in designing new approaches to intervene during viral infection or to harness TEVs as therapeutic agents.
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Affiliation(s)
- Kunihiro Uryu
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
- Janelia Rearch Campsu, Ashuburn, Virginia, 20147, USA
| | - Nadine Soplop
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Timothy P. Sheahan
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065 USA
| | - Maria-Teresa Catanese
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065 USA
| | - Chuong Huynh
- Ion Microscopy Innovation Center, Zeiss Microscopy LLC, Peabody, MA 01960, USA
| | - John Pena
- Sonder Research X, Cornell University, Ithaca, NY 14853, USA
| | - Nancy Boudreau
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065 USA
| | - Irina Matei
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065 USA
| | - Candia Kenific
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065 USA
| | - Ayako Hashimoto
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065 USA
| | - Ayuko Hoshino
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065 USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065 USA
| | - David Lyden
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065 USA
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Okada T, Iwayama T, Ogura T, Murakami S, Ogura T. Structural analysis of melanosomes in living mammalian cells using scanning electron-assisted dielectric microscopy with deep neural network. Comput Struct Biotechnol J 2022; 21:506-518. [PMID: 36618988 PMCID: PMC9807747 DOI: 10.1016/j.csbj.2022.12.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Melanins are the main pigments found in mammals. Their synthesis and transfer to keratinocytes have been widely investigated for many years. However, analysis has been mainly carried out using fixed rather than live cells. In this study, we have analysed the melanosomes in living mammalian cells using newly developed scanning electron-assisted dielectric microscopy (SE-ADM). The melanosomes in human melanoma MNT-1 cells were observed as clear black particles in SE-ADM. The main structure of melanosomes was toroidal while that of normal melanocytes was ellipsoidal. In tyrosinase knockout MNT-1 cells, not only the black particles in the SE-ADM images but also the Raman shift of melanin peaks completely disappeared suggesting that the black particles were really melanosomes. We developed a deep neural network (DNN) system to automatically detect melanosomes in cells and analysed their diameter and roundness. In terms of melanosome morphology, the diameter of melanosomes in melanoma cells did not change while that in normal melanocytes increased during culture. The established DNN analysis system with SE-ADM can be used for other particles, e.g. exosomes, lysosomes, and other biological particles.
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Affiliation(s)
- Tomoko Okada
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Tomoaki Iwayama
- Department of Periodontology, Osaka University Graduate School of Dentistry, 1-8 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Taku Ogura
- Chemical Business Unit, Nikko Chemicals Co., Ltd., Itabashi-ku, Tokyo 174-0046, Japan
| | - Shinya Murakami
- Department of Periodontology, Osaka University Graduate School of Dentistry, 1-8 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Toshihiko Ogura
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi, Tsukuba, Ibaraki 305-8566, Japan,Correspondence to: Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan.
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Ogura T. Development of multi-frequency impedance scanning electron microscopy. PLoS One 2022; 17:e0263098. [PMID: 35077509 PMCID: PMC8789111 DOI: 10.1371/journal.pone.0263098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/11/2022] [Indexed: 11/23/2022] Open
Abstract
Nanometre-scale observation of specimens in water is indispensable in many scientific fields like biology, chemistry, material science and nanotechnology. Scanning electron microscopy (SEM) allows high-resolution images of biological samples to be obtained under high vacuum conditions but requires specific sample-preparation protocols. Therefore, there is a need for convenient and minimally invasive methods of observing samples in solution. We have developed a new type of impedance microscopy, namely multi-frequency impedance SEM (IP-SEM), which allows nanoscale imaging of various specimens in water while minimising radiation damage. By varying the frequency of the input voltage signal of the sine wave, the present system can detect dielectric properties of the sample’s composition at nanometre resolution. It also enables examination of unstained biological specimens and material samples in water. Furthermore, it can be used for diverse samples in liquids across a broad range of scientific subjects such as nanoparticles, nanotubes and organic and catalytic materials.
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Affiliation(s)
- Toshihiko Ogura
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- * E-mail:
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