1
|
Korelin K, Oostveen M, Wahbi W, Ianevski F, Cavalcante B, Turunen L, Belevich I, Al-Samadi A, Salo T. Evaluation of BH3 mimetics as a combination therapy with irradiation in head and neck squamous cell carcinoma. Biomed Pharmacother 2024; 175:116719. [PMID: 38749173 DOI: 10.1016/j.biopha.2024.116719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 06/03/2024] Open
Abstract
INTRODUCTION Head and neck squamous cell carcinoma (HNSCC) is a common cancer with a five-year survival rate around 60%, indicating a need for new treatments. BH3 mimetics are small molecules that inhibit anti-apoptotic Bcl-2 family proteins, resulting in apoptosis induction. METHODS We performed a high-throughput screen using a Myogel matrix to identify the synergy between irradiation and the novel BH3 mimetics A-1155463, A-1331852, and navitoclax in 12 HNSCC cell lines, normal (NOF) and cancer-associated fibroblasts (CAF), and dysplastic keratinocytes (ODA). Next, we examined synergy in an apoptosis assay, followed by a clonogenic assay and a Myogel spheroid on selected HNSCC cell lines. Finally, we applied zebrafish larvae xenograft to validate the effects of navitoclax and A-1331852. RESULTS All three BH3 mimetics exhibited a strong synergy with irradiation in eight HNSCC cell lines and ODAs, but not in NOFs and CAFs. A-1155463 and A-1331852 induced apoptosis and reduced proliferation, and together with irradiation, significantly increased apoptosis and arrested proliferation. A-1331852 and navitoclax significantly decreased the clonogenicity compared with the control, and combination treatment led to a decreased clonogenicity compared with monotherapy or irradiation. However, unlike navitoclax or A-1155463, only A-1331852 significantly reduced cancer cell invasion. Furthermore, in spheroid and zebrafish, irradiation appeared ineffective and failed to significantly increase the drug effect. In the zebrafish, A-1331852 and navitoclax significantly reduced the tumor area and metastasis. CONCLUSIONS Our findings encourage the further preclinical investigation of BH3 mimetics, particularly A-1331852, as a single agent or combined with irradiation as a treatment for HNSCC.
Collapse
Affiliation(s)
- Katja Korelin
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki 00014, Finland; Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Mayke Oostveen
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki 00014, Finland
| | - Wafa Wahbi
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki 00014, Finland; Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki 00014, Finland
| | - Filipp Ianevski
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland
| | - Bruno Cavalcante
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki 00014, Finland; Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador 40296-710, Brazil; Department of Pathology and Forensic Medicine, School of Medicine, Federal University of Bahia, Salvador 40110-909, Brazil
| | - Laura Turunen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Ahmed Al-Samadi
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki 00014, Finland; Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki 00014, Finland; Institute of Dentistry, School of Medicine, Kuopio Campus, University of Eastern Finland, Kuopio, Finland
| | - Tuula Salo
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki 00014, Finland; Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki 00014, Finland; Cancer and Translational Medicine Research Unit, University of Oulu, Oulu 90014, Finland; Medical Research Center, Oulu University Hospital, Oulu 90220, Finland; Department of Pathology, Helsinki University Hospital (HUS), Helsinki 00029, Finland
| |
Collapse
|
2
|
Matsumoto M, Matsushita K, Hane M, Wen C, Kurematsu C, Ota H, Bang Nguyen H, Quynh Thai T, Herranz-Pérez V, Sawada M, Fujimoto K, García-Verdugo JM, Kimura KD, Seki T, Sato C, Ohno N, Sawamoto K. Neuraminidase inhibition promotes the collective migration of neurons and recovery of brain function. EMBO Mol Med 2024:10.1038/s44321-024-00073-7. [PMID: 38789599 DOI: 10.1038/s44321-024-00073-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
In the injured brain, new neurons produced from endogenous neural stem cells form chains and migrate to injured areas and contribute to the regeneration of lost neurons. However, this endogenous regenerative capacity of the brain has not yet been leveraged for the treatment of brain injury. Here, we show that in healthy brain chains of migrating new neurons maintain unexpectedly large non-adherent areas between neighboring cells, allowing for efficient migration. In instances of brain injury, neuraminidase reduces polysialic acid levels, which negatively regulates adhesion, leading to increased cell-cell adhesion and reduced migration efficiency. The administration of zanamivir, a neuraminidase inhibitor used for influenza treatment, promotes neuronal migration toward damaged regions, fosters neuronal regeneration, and facilitates functional recovery. Together, these findings shed light on a new mechanism governing efficient neuronal migration in the adult brain under physiological conditions, pinpoint the disruption of this mechanism during brain injury, and propose a promising therapeutic avenue for brain injury through drug repositioning.
Collapse
Affiliation(s)
- Mami Matsumoto
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
- Division of Neural Development and Regeneration, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan
| | - Katsuyoshi Matsushita
- Department of Mathematical and Life Sciences, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Masaya Hane
- Bioscience and Biotechnology Center, Graduate School of Bioagricultural Sciences, and Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8601, Japan
| | - Chentao Wen
- Graduate School of Science, Nagoya City University, Nagoya, 467-8501, Japan
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan
| | - Chihiro Kurematsu
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
| | - Haruko Ota
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
- Department of Anesthesiology and Intensive Care Medicine, Graduate School of Medical Sciences, Nagoya City University, Nagoya, 467-8601, Japan
| | - Huy Bang Nguyen
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, 444-8787, Japan
- Department of Anatomy, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City (UMP), Ho Chi Minh City, 70000, Vietnam
| | - Truc Quynh Thai
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, 444-8787, Japan
- Department of Histology-Embryology-Genetics, Faculty of Basic Medical Sciences, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, 70000, Vietnam
| | - Vicente Herranz-Pérez
- Laboratory of Comparative Neurobiology, Cavanilles Institute, University of Valencia, CIBERNED-ISCIII, Valencia, 46980, Spain
- Department of Cell Biology, Functional Biology and Physical Anthropology, University of Valencia, Burjassot, 46100, Spain
| | - Masato Sawada
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
- Division of Neural Development and Regeneration, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan
| | - Koichi Fujimoto
- Department of Mathematical and Life Sciences, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - José Manuel García-Verdugo
- Laboratory of Comparative Neurobiology, Cavanilles Institute, University of Valencia, CIBERNED-ISCIII, Valencia, 46980, Spain
| | - Koutarou D Kimura
- Graduate School of Science, Nagoya City University, Nagoya, 467-8501, Japan
| | - Tatsunori Seki
- Department of Histology and Neuroanatomy, Tokyo Medical University, Tokyo, 160-8402, Japan
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo, 160-8402, Japan
| | - Chihiro Sato
- Bioscience and Biotechnology Center, Graduate School of Bioagricultural Sciences, and Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8601, Japan
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, Jichi Medical University, Shimotsuke, 329-0498, Japan
- Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan
| | - Kazunobu Sawamoto
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan.
- Division of Neural Development and Regeneration, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan.
| |
Collapse
|
3
|
Ikeda KN, Belevich I, Zelaya-Lainez L, Orel L, Füssl J, Gumulec J, Hellmich C, Jokitalo E, Raible F. Dynamic microvilli sculpt bristles at nanometric scale. Nat Commun 2024; 15:3733. [PMID: 38740737 DOI: 10.1038/s41467-024-48044-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 04/19/2024] [Indexed: 05/16/2024] Open
Abstract
Organisms generate shapes across size scales. Whereas patterning and morphogenesis of macroscopic tissues has been extensively studied, the principles underlying the formation of micrometric and submicrometric structures remain largely enigmatic. Individual cells of polychaete annelids, so-called chaetoblasts, are associated with the generation of chitinous bristles of highly stereotypic geometry. Here we show that bristle formation requires a chitin-producing enzyme specifically expressed in the chaetoblasts. Chaetoblasts exhibit dynamic cell surfaces with stereotypical patterns of actin-rich microvilli. These microvilli can be matched with internal and external structures of bristles reconstructed from serial block-face electron micrographs. Individual chitin teeth are deposited by microvilli in an extension-disassembly cycle resembling a biological 3D printer. Consistently, pharmacological interference with actin dynamics leads to defects in tooth formation. Our study reveals that both material and shape of bristles are encoded by the same cell, and that microvilli play a role in micro- to submicrometric sculpting of biomaterials.
Collapse
Affiliation(s)
- Kyojiro N Ikeda
- Max Perutz Labs; University of Vienna, 1030, Vienna, Austria.
| | - Ilya Belevich
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Luis Zelaya-Lainez
- Institute for Mechanics of Materials and Structures, TU Wien-Vienna University of Technology, Vienna, Austria
| | - Lukas Orel
- Max Perutz Labs; University of Vienna, 1030, Vienna, Austria
| | - Josef Füssl
- Institute for Mechanics of Materials and Structures, TU Wien-Vienna University of Technology, Vienna, Austria
| | - Jaromír Gumulec
- Department of Pathophysiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Christian Hellmich
- Institute for Mechanics of Materials and Structures, TU Wien-Vienna University of Technology, Vienna, Austria
| | - Eija Jokitalo
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Florian Raible
- Max Perutz Labs; University of Vienna, 1030, Vienna, Austria.
- Research Platform "Single-Cell Regulation of Stem Cells", University of Vienna, Vienna, Austria.
| |
Collapse
|
4
|
Murase S, Mantani Y, Ohno N, Shimada A, Nakanishi S, Morishita R, Yokoyama T, Hoshi N. Regional differences in the ultrastructure of mucosal macrophages in the rat large intestine. Cell Tissue Res 2024; 396:245-253. [PMID: 38485763 DOI: 10.1007/s00441-024-03883-w] [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] [Received: 09/06/2023] [Accepted: 02/25/2024] [Indexed: 04/28/2024]
Abstract
We previously clarified the histological characteristics of macrophages in the rat small intestine using serial block-face scanning electron microscopy (SBF-SEM). However, the regional differences in the characteristics of macrophages throughout the large intestine remain unknown. Here, we performed a pilot study to explore the regional differences in the ultrastructure of mucosal macrophages in the large intestine by using SBF-SEM analysis. SBF-SEM analysis conducted on the luminal side of the cecum and descending colon revealed macrophages as amorphous cells possessing abundant lysosomes and vacuoles. Macrophages in the cecum exhibited a higher abundance of lysosomes and a lower abundance of vacuoles than those in the descending colon. Macrophages with many intraepithelial cellular processes were observed beneath the intestinal superficial epithelium in the descending colon. Moreover, macrophages in contact with nerve fibers were more prevalent in the cecum than in the descending colon, and a subset of them surrounded a nerve bundle only in the cecum. In conclusion, the present pilot study suggested that the quantity of some organelles (lysosomes and vacuoles) in macrophages differed between the cecum and the descending colon and that there were some region-specific subsets of macrophages like nerve-associated macrophages in the cecum.
Collapse
Affiliation(s)
- Shota Murase
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan
| | - Youhei Mantani
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan.
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, Jichi Medical University, School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
- Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, Aichi, 444-8787, Japan
| | - Asaka Shimada
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan
| | - Satoki Nakanishi
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan
| | - Rinako Morishita
- Laboratory of Histophysiology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan
| | - Toshifumi Yokoyama
- Laboratory of Animal Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan
| | - Nobuhiko Hoshi
- Laboratory of Animal Molecular Morphology, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-Cho, Nada-Ku, Kobe, Hyogo, 657-8501, Japan
| |
Collapse
|
5
|
Müller A, Schmidt D, Albrecht JP, Rieckert L, Otto M, Galicia Garcia LE, Fabig G, Solimena M, Weigert M. Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets. Nat Protoc 2024; 19:1436-1466. [PMID: 38424188 DOI: 10.1038/s41596-024-00957-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/24/2023] [Indexed: 03/02/2024]
Abstract
Volume electron microscopy is the method of choice for the in situ interrogation of cellular ultrastructure at the nanometer scale, and with the increase in large raw image datasets generated, improving computational strategies for image segmentation and spatial analysis is necessary. Here we describe a practical and annotation-efficient pipeline for organelle-specific segmentation, spatial analysis and visualization of large volume electron microscopy datasets using freely available, user-friendly software tools that can be run on a single standard workstation. The procedures are aimed at researchers in the life sciences with modest computational expertise, who use volume electron microscopy and need to generate three-dimensional (3D) segmentation labels for different types of cell organelles while minimizing manual annotation efforts, to analyze the spatial interactions between organelle instances and to visualize the 3D segmentation results. We provide detailed guidelines for choosing well-suited segmentation tools for specific cell organelles, and to bridge compatibility issues between freely available open-source tools, we distribute the critical steps as easily installable Album solutions for deep learning segmentation, spatial analysis and 3D rendering. Our detailed description can serve as a reference for similar projects requiring particular strategies for single- or multiple-organelle analysis, which can be achieved with computational resources commonly available to single-user setups.
Collapse
Affiliation(s)
- Andreas Müller
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany.
- German Center for Diabetes Research, Neuherberg, Germany.
| | - Deborah Schmidt
- HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.
| | - Jan Philipp Albrecht
- HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
- Humboldt-Universität zu Berlin, Faculty of Mathematics and Natural Sciences, Berlin, Germany
| | - Lucas Rieckert
- HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Maximilian Otto
- HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Leticia Elizabeth Galicia Garcia
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- DFG Cluster of Excellence 'Physics of Life', TU Dresden, Dresden, Germany
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Dresden, Dresden, Germany
| | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- DFG Cluster of Excellence 'Physics of Life', TU Dresden, Dresden, Germany
| | - Martin Weigert
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| |
Collapse
|
6
|
Chechekhina E, Voloshin N, Kulebyakin K, Tyurin-Kuzmin P. Code-Free Machine Learning Solutions for Microscopy Image Processing: Deep Learning. Tissue Eng Part A 2024. [PMID: 38556835 DOI: 10.1089/ten.tea.2024.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024] Open
Abstract
In recent years, there has been a significant expansion in the realm of processing microscopy images, thanks to the advent of machine learning techniques. These techniques offer diverse applications for image processing. Currently, numerous methods are used for processing microscopy images in the field of biology, ranging from conventional machine learning algorithms to sophisticated deep learning artificial neural networks with millions of parameters. However, a comprehensive grasp of the intricacies of these methods usually necessitates proficiency in programming and advanced mathematics. In our comprehensive review, we explore various widely used deep learning approaches tailored for the processing of microscopy images. Our emphasis is on algorithms that have gained popularity in the field of biology and have been adapted to cater to users lacking programming expertise. In essence, our target audience comprises biologists interested in exploring the potential of deep learning algorithms, even without programming skills. Throughout the review, we elucidate each algorithm's fundamental concepts and capabilities without delving into mathematical and programming complexities. Crucially, all the highlighted algorithms are accessible on open platforms without requiring code, and we provide detailed descriptions and links within our review. It's essential to recognize that addressing each specific problem demands an individualized approach. Consequently, our focus is not on comparing algorithms but on delineating the problems they are adept at solving. In practical scenarios, researchers typically select multiple algorithms suited to their tasks and experimentally determine the most effective one. It is worth noting that microscopy extends beyond the realm of biology; its applications span diverse fields such as geology and material science. Although our review predominantly centers on biomedical applications, the algorithms and principles outlined here are equally applicable to other scientific domains. Furthermore, a number of the proposed solutions can be modified for use in entirely distinct computer vision cases.
Collapse
Affiliation(s)
- Elizaveta Chechekhina
- Department of Biochemistry and Regenerative Biomedicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Nikita Voloshin
- Department of Biochemistry and Regenerative Biomedicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin Kulebyakin
- Department of Biochemistry and Regenerative Biomedicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Pyotr Tyurin-Kuzmin
- Department of Biochemistry and Regenerative Biomedicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
7
|
Leclerc S, Gupta A, Ruokolainen V, Chen JH, Kunnas K, Ekman AA, Niskanen H, Belevich I, Vihinen H, Turkki P, Perez-Berna AJ, Kapishnikov S, Mäntylä E, Harkiolaki M, Dufour E, Hytönen V, Pereiro E, McEnroe T, Fahy K, Kaikkonen MU, Jokitalo E, Larabell CA, Weinhardt V, Mattola S, Aho V, Vihinen-Ranta M. Progression of herpesvirus infection remodels mitochondrial organization and metabolism. PLoS Pathog 2024; 20:e1011829. [PMID: 38620036 PMCID: PMC11045090 DOI: 10.1371/journal.ppat.1011829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/25/2024] [Accepted: 03/12/2024] [Indexed: 04/17/2024] Open
Abstract
Viruses target mitochondria to promote their replication, and infection-induced stress during the progression of infection leads to the regulation of antiviral defenses and mitochondrial metabolism which are opposed by counteracting viral factors. The precise structural and functional changes that underlie how mitochondria react to the infection remain largely unclear. Here we show extensive transcriptional remodeling of protein-encoding host genes involved in the respiratory chain, apoptosis, and structural organization of mitochondria as herpes simplex virus type 1 lytic infection proceeds from early to late stages of infection. High-resolution microscopy and interaction analyses unveiled infection-induced emergence of rough, thin, and elongated mitochondria relocalized to the perinuclear area, a significant increase in the number and clustering of endoplasmic reticulum-mitochondria contact sites, and thickening and shortening of mitochondrial cristae. Finally, metabolic analyses demonstrated that reactivation of ATP production is accompanied by increased mitochondrial Ca2+ content and proton leakage as the infection proceeds. Overall, the significant structural and functional changes in the mitochondria triggered by the viral invasion are tightly connected to the progression of the virus infection.
Collapse
Affiliation(s)
- Simon Leclerc
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Alka Gupta
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Visa Ruokolainen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Kari Kunnas
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Axel A. Ekman
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Henri Niskanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Paula Turkki
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ana J. Perez-Berna
- MISTRAL Beamline-Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Valles, Barcelona, Spain
| | | | - Elina Mäntylä
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK; Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, United Kingdom
| | - Eric Dufour
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vesa Hytönen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab laboratories, Tampere, Finland
| | - Eva Pereiro
- MISTRAL Beamline-Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Valles, Barcelona, Spain
| | | | | | - Minna U. Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Carolyn A. Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Venera Weinhardt
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Salla Mattola
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Vesa Aho
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Maija Vihinen-Ranta
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| |
Collapse
|
8
|
Lachiondo-Ortega S, Rejano-Gordillo CM, Simon J, Lopitz-Otsoa F, C Delgado T, Mazan-Mamczarz K, Goikoetxea-Usandizaga N, Zapata-Pavas LE, García-Del Río A, Guerra P, Peña-Sanfélix P, Hermán-Sánchez N, Al-Abdulla R, Fernandez-Rodríguez C, Azkargorta M, Velázquez-Cruz A, Guyon J, Martín C, Zalamea JD, Egia-Mendikute L, Sanz-Parra A, Serrano-Maciá M, González-Recio I, Gonzalez-Lopez M, Martínez-Cruz LA, Pontisso P, Aransay AM, Barrio R, Sutherland JD, Abrescia NGA, Elortza F, Lujambio A, Banales JM, Luque RM, Gahete MD, Palazón A, Avila MA, G Marin JJ, De S, Daubon T, Díaz-Quintana A, Díaz-Moreno I, Gorospe M, Rodríguez MS, Martínez-Chantar ML. SUMOylation controls Hu antigen R posttranscriptional activity in liver cancer. Cell Rep 2024; 43:113924. [PMID: 38507413 PMCID: PMC11025316 DOI: 10.1016/j.celrep.2024.113924] [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] [Received: 09/30/2022] [Revised: 08/08/2023] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
The posttranslational modification of proteins critically influences many biological processes and is a key mechanism that regulates the function of the RNA-binding protein Hu antigen R (HuR), a hub in liver cancer. Here, we show that HuR is SUMOylated in the tumor sections of patients with hepatocellular carcinoma in contrast to the surrounding tissue, as well as in human cell line and mouse models of the disease. SUMOylation of HuR promotes major cancer hallmarks, namely proliferation and invasion, whereas the absence of HuR SUMOylation results in a senescent phenotype with dysfunctional mitochondria and endoplasmic reticulum. Mechanistically, SUMOylation induces a structural rearrangement of the RNA recognition motifs that modulates HuR binding affinity to its target RNAs, further modifying the transcriptomic profile toward hepatic tumor progression. Overall, SUMOylation constitutes a mechanism of HuR regulation that could be potentially exploited as a therapeutic strategy for liver cancer.
Collapse
Affiliation(s)
- Sofia Lachiondo-Ortega
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Claudia M Rejano-Gordillo
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Extremadura, University Institute of Biosanitary Research of Extremadura (INUBE), 06071 Badajoz, Spain; Biofisika Institute, Consejo Superior de Investigaciones Científicas (CSIC), Departamento Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Jorge Simon
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain
| | - Fernando Lopitz-Otsoa
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Teresa C Delgado
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Naroa Goikoetxea-Usandizaga
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - L Estefanía Zapata-Pavas
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Ana García-Del Río
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Pietro Guerra
- Unit of Internal Medicine and Hepatology (UIMH), Department of Medicine (DIMED), University of Padova, 35128 Padua, Italy
| | - Patricia Peña-Sanfélix
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Natalia Hermán-Sánchez
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Ruba Al-Abdulla
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández, Elche, Spain; Institute of Medical Biochemistry and Molecular Biology, University Medicine of Greifswald, 17475 Greifswald, Germany
| | - Carmen Fernandez-Rodríguez
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Proteomics Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), 48160 Derio, Bizkaia, Spain
| | - Alejandro Velázquez-Cruz
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Joris Guyon
- University of Bordeaux, INSERM, BPH, U1219, 33000 Bordeaux, France; CHU de Bordeaux, Service de Pharmacologie Médicale, 33000 Bordeaux, France
| | - César Martín
- Biofisika Institute, Consejo Superior de Investigaciones Científicas (CSIC), Departamento Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Juan Diego Zalamea
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Leire Egia-Mendikute
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Arantza Sanz-Parra
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Marina Serrano-Maciá
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Irene González-Recio
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Monika Gonzalez-Lopez
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Luis Alfonso Martínez-Cruz
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Patrizia Pontisso
- Unit of Internal Medicine and Hepatology (UIMH), Department of Medicine (DIMED), University of Padova, 35128 Padua, Italy
| | - Ana M Aransay
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Rosa Barrio
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - James D Sutherland
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Nicola G A Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Félix Elortza
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Proteomics Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Carlos III Networked Proteomics Platform (ProteoRed-ISCIII), 48160 Derio, Bizkaia, Spain
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jesus M Banales
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain; Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, San Sebastian, Spain; Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Raúl M Luque
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Manuel D Gahete
- Maimónides Institute of Biomedical Research of Córdoba (IMIBIC), Department of Cell Biology, Physiology and Immunology of University of Córdoba, Reina Sofia University Hospital, CIBER Pathophysiology of Obesity and Nutrition (CIBERobn), 14004 Córdoba, Spain
| | - Asís Palazón
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Matias A Avila
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Hepatology Program, Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Pamplona, Spain; Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Pamplona, Spain
| | - Jose J G Marin
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain; Experimental Hepatology and Drug Targeting (HEVEPHARM), Instituto de Investigación Biomédica de Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Thomas Daubon
- University of Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Manuel S Rodríguez
- Laboratoire de Chimie de Coordination (LCC), UPR 8241, CNRS; IPBS-University of Toulouse III-Paul Sabatier, Toulouse, France
| | - María Luz Martínez-Chantar
- Liver Disease Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, Madrid, Spain.
| |
Collapse
|
9
|
Xu J, Liao C, Yin CC, Li G, Zhu Y, Sun F. In situ structural insights into the excitation-contraction coupling mechanism of skeletal muscle. SCIENCE ADVANCES 2024; 10:eadl1126. [PMID: 38507485 PMCID: PMC10954225 DOI: 10.1126/sciadv.adl1126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/12/2024] [Indexed: 03/22/2024]
Abstract
Excitation-contraction coupling (ECC) is a fundamental mechanism in control of skeletal muscle contraction and occurs at triad junctions, where dihydropyridine receptors (DHPRs) on transverse tubules sense excitation signals and then cause calcium release from the sarcoplasmic reticulum via coupling to type 1 ryanodine receptors (RyR1s), inducing the subsequent contraction of muscle filaments. However, the molecular mechanism remains unclear due to the lack of structural details. Here, we explored the architecture of triad junction by cryo-electron tomography, solved the in situ structure of RyR1 in complex with FKBP12 and calmodulin with the resolution of 16.7 Angstrom, and found the intact RyR1-DHPR supercomplex. RyR1s arrange into two rows on the terminal cisternae membrane by forming right-hand corner-to-corner contacts, and tetrads of DHPRs bind to RyR1s in an alternating manner, forming another two rows on the transverse tubule membrane. This unique arrangement is important for synergistic calcium release and provides direct evidence of physical coupling in ECC.
Collapse
Affiliation(s)
- Jiashu Xu
- Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenyi Liao
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chang-Cheng Yin
- Department of Biophysics, The Health Science Center, Peking University, Beijing 100191, China
- Electron Microscopy Analysis Laboratory, The Health Science Center, Peking University, Beijing 100191, China
- Center for Protein Science, Peking University, Beijing 100871, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yun Zhu
- Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Sun
- Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, 510005, China
| |
Collapse
|
10
|
Tomasch J, Kopejtka K, Bílý T, Gardiner AT, Gardian Z, Shivaramu S, Koblížek M, Kaftan D. A photoheterotrophic bacterium from Iceland has adapted its photosynthetic machinery to the long days of polar summer. mSystems 2024; 9:e0131123. [PMID: 38376261 PMCID: PMC10949492 DOI: 10.1128/msystems.01311-23] [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] [Received: 12/05/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
During their long evolution, anoxygenic phototrophic bacteria have inhabited a wide variety of natural habitats and developed specific strategies to cope with the challenges of any particular environment. Expression, assembly, and safe operation of the photosynthetic apparatus must be regulated to prevent reactive oxygen species generation under illumination in the presence of oxygen. Here, we report on the photoheterotrophic Sediminicoccus sp. strain KRV36, which was isolated from a cold stream in north-western Iceland, 30 km south of the Arctic Circle. In contrast to most aerobic anoxygenic phototrophs, which stop pigment synthesis when illuminated, strain KRV36 maintained its bacteriochlorophyll synthesis even under continuous light. Its cells also contained between 100 and 180 chromatophores, each accommodating photosynthetic complexes that exhibit an unusually large carotenoid absorption spectrum. The expression of photosynthesis genes in dark-adapted cells was transiently downregulated in the first 2 hours exposed to light but recovered to the initial level within 24 hours. An excess of membrane-bound carotenoids as well as high, constitutive expression of oxidative stress response genes provided the required potential for scavenging reactive oxygen species, safeguarding bacteriochlorophyll synthesis and photosystem assembly. The unique cellular architecture and an unusual gene expression pattern represent a specific adaptation that allows the maintenance of anoxygenic phototrophy under arctic conditions characterized by long summer days with relatively low irradiance.IMPORTANCEThe photoheterotrophic bacterium Sediminicoccus sp. KRV36 was isolated from a cold stream in Iceland. It expresses its photosynthesis genes, synthesizes bacteriochlorophyll, and assembles functional photosynthetic complexes under continuous light in the presence of oxygen. Unraveling the molecular basis of this ability, which is exceptional among aerobic anoxygenic phototrophic species, will help to understand the evolution of bacterial photosynthesis in response to changing environmental conditions. It might also open new possibilities for genetic engineering of biotechnologically relevant phototrophs, with the aim of increasing photosynthetic activity and their tolerance to reactive oxygen species.
Collapse
Affiliation(s)
- Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Tomáš Bílý
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Alastair T. Gardiner
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Zdenko Gardian
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Sahana Shivaramu
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - David Kaftan
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department Chemistry, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| |
Collapse
|
11
|
Franzkoch R, Anand A, Breitsprecher L, Psathaki OE, Barisch C. Resolving exit strategies of mycobacteria in Dictyostelium discoideum by combining high-pressure freezing with 3D-correlative light and electron microscopy. Mol Microbiol 2024; 121:593-604. [PMID: 38063129 DOI: 10.1111/mmi.15205] [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] [Received: 05/15/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 03/12/2024]
Abstract
The infection course of Mycobacterium tuberculosis is highly dynamic and comprises sequential stages that require damaging and crossing of several membranes to enable the translocation of the bacteria into the cytosol or their escape from the host. Many important breakthroughs such as the restriction of mycobacteria by the autophagy pathway and the recruitment of sophisticated host repair machineries to the Mycobacterium-containing vacuole have been gained in the Dictyostelium discoideum/M. marinum system. Despite the availability of well-established light and advanced electron microscopy techniques in this system, a correlative approach integrating both methods with near-native ultrastructural preservation is currently lacking. This is most likely due to the low ability of D. discoideum to adhere to surfaces, which results in cell loss even after fixation. To address this problem, we improved the adhesion of cells and developed a straightforward and convenient workflow for 3D-correlative light and electron microscopy. This approach includes high-pressure freezing, which is an excellent technique for preserving membranes. Thus, our method allows to monitor the ultrastructural aspects of vacuole escape which is of central importance for the survival and dissemination of bacterial pathogens.
Collapse
Affiliation(s)
- Rico Franzkoch
- iBiOs-integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics, Osnabrück, Germany
- Division of Microbiology, Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Aby Anand
- Center of Cellular Nanoanalytics, Osnabrück, Germany
- Division of Molecular Infection Biology, Department of Biology, University of Osnabrück, Osnabrück, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Division of Host-Microbe Interactome, Research Center Borstel - Leibniz Lung Center (FZB), Borstel, Germany
- Department of Biology, University of Hamburg, Hamburg, Germany
| | - Leonhard Breitsprecher
- iBiOs-integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics, Osnabrück, Germany
- Division of Microbiology, Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Olympia E Psathaki
- iBiOs-integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics, Osnabrück, Germany
| | - Caroline Barisch
- Center of Cellular Nanoanalytics, Osnabrück, Germany
- Division of Molecular Infection Biology, Department of Biology, University of Osnabrück, Osnabrück, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Division of Host-Microbe Interactome, Research Center Borstel - Leibniz Lung Center (FZB), Borstel, Germany
- Department of Biology, University of Hamburg, Hamburg, Germany
| |
Collapse
|
12
|
Lee A, Sung G, Shin S, Lee SY, Sim J, Nhung TTM, Nghi TD, Park SK, Sathieshkumar PP, Kang I, Mun JY, Kim JS, Rhee HW, Park KM, Kim K. OrthoID: profiling dynamic proteomes through time and space using mutually orthogonal chemical tools. Nat Commun 2024; 15:1851. [PMID: 38424052 PMCID: PMC10904832 DOI: 10.1038/s41467-024-46034-z] [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] [Received: 04/12/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Identifying proteins at organelle contact sites, such as mitochondria-associated endoplasmic reticulum membranes (MAM), is essential for understanding vital cellular processes, yet challenging due to their dynamic nature. Here we report "OrthoID", a proteomic method utilizing engineered enzymes, TurboID and APEX2, for the biotinylation (Bt) and adamantylation (Ad) of proteins close to the mitochondria and endoplasmic reticulum (ER), respectively, in conjunction with high-affinity binding pairs, streptavidin-biotin (SA-Bt) and cucurbit[7]uril-adamantane (CB[7]-Ad), for selective orthogonal enrichment of Bt- and Ad-labeled proteins. This approach effectively identifies protein candidates associated with the ER-mitochondria contact, including LRC59, whose roles at the contact site were-to the best of our knowledge-previously unknown, and tracks multiple protein sets undergoing structural and locational changes at MAM during mitophagy. These findings demonstrate that OrthoID could be a powerful proteomics tool for the identification and analysis of spatiotemporal proteins at organelle contact sites and revealing their dynamic behaviors in vital cellular processes.
Collapse
Affiliation(s)
- Ara Lee
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, Republic of Korea
- Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Gihyun Sung
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, Republic of Korea
- Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Sanghee Shin
- Center for RNA Research, Institute for Basic Science (IBS), Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Song-Yi Lee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jaehwan Sim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Truong Thi My Nhung
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Tran Diem Nghi
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | | | - Imkyeung Kang
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
- Department of Microbiology, University of Ulsan College of Medicine, Ulsan, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea.
| | - Kyeng Min Park
- Department of Biochemistry, Daegu Catholic University School of Medicine, Daegu, Republic of Korea.
| | - Kimoon Kim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, Republic of Korea.
- Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
| |
Collapse
|
13
|
Jan M, Spangaro A, Lenartowicz M, Mattiazzi Usaj M. From pixels to insights: Machine learning and deep learning for bioimage analysis. Bioessays 2024; 46:e2300114. [PMID: 38058114 DOI: 10.1002/bies.202300114] [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] [Received: 06/24/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 12/08/2023]
Abstract
Bioimage analysis plays a critical role in extracting information from biological images, enabling deeper insights into cellular structures and processes. The integration of machine learning and deep learning techniques has revolutionized the field, enabling the automated, reproducible, and accurate analysis of biological images. Here, we provide an overview of the history and principles of machine learning and deep learning in the context of bioimage analysis. We discuss the essential steps of the bioimage analysis workflow, emphasizing how machine learning and deep learning have improved preprocessing, segmentation, feature extraction, object tracking, and classification. We provide examples that showcase the application of machine learning and deep learning in bioimage analysis. We examine user-friendly software and tools that enable biologists to leverage these techniques without extensive computational expertise. This review is a resource for researchers seeking to incorporate machine learning and deep learning in their bioimage analysis workflows and enhance their research in this rapidly evolving field.
Collapse
Affiliation(s)
- Mahta Jan
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
| | - Allie Spangaro
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
| | - Michelle Lenartowicz
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
| | - Mojca Mattiazzi Usaj
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
| |
Collapse
|
14
|
Rahman SMT, Zhou W, Deiters A, Haugh JM. Dissection of MKK6 and p38 Signaling Using Light-Activated Protein Kinases. Chembiochem 2024; 25:e202300551. [PMID: 37856284 DOI: 10.1002/cbic.202300551] [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] [Received: 08/04/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Abstract
Stress-activated signaling pathways orchestrate cellular behaviors and fates. Studying the precise role(s) of stress-activated protein kinases is challenging, because stress conditions induce adaptation and impose selection pressure. To meet this challenge, we have applied an optogenetic system with a single plasmid to express light-activated p38α or its upstream activator, MKK6, in conjunction with live-cell fluorescence microscopy. In starved cells, decaging of constitutively active p38α or MKK6 by brief exposure to UV light elicits rapid p38-mediated signaling, release of cytochrome c from mitochondria, and apoptosis with different kinetics. In parallel, light activation of p38α also suppresses autophagosome formation, similarly to stimulation with growth factors that activate PI3K/Akt/mTORC1 signaling. Active MKK6 negatively regulates serum-induced ERK activity, which is p38-independent as previously reported. Here, we reproduce that result with the one plasmid system and show that although decaging active p38α does not reduce basal ERK activity in our cells, it can block growth factor-stimulated ERK signaling in serum-starved cells. These results clarify the roles of MKK6 and p38α in dynamic signaling programs, which act in concert to actuate apoptotic death while suppressing cell survival mechanisms.
Collapse
Affiliation(s)
- Shah Md Toufiqur Rahman
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Wenyuan Zhou
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jason M Haugh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, 911 Partners Way, Raleigh, NC, 27695, USA
| |
Collapse
|
15
|
Machireddy A, Thibault G, Loftis KG, Stoltz K, Bueno CE, Smith HR, Riesterer JL, Gray JW, Song X. Segmentation of cellular ultrastructures on sparsely labeled 3D electron microscopy images using deep learning. FRONTIERS IN BIOINFORMATICS 2023; 3:1308708. [PMID: 38162124 PMCID: PMC10754953 DOI: 10.3389/fbinf.2023.1308708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024] Open
Abstract
Focused ion beam-scanning electron microscopy (FIB-SEM) images can provide a detailed view of the cellular ultrastructure of tumor cells. A deeper understanding of their organization and interactions can shed light on cancer mechanisms and progression. However, the bottleneck in the analysis is the delineation of the cellular structures to enable quantitative measurements and analysis. We mitigated this limitation using deep learning to segment cells and subcellular ultrastructure in 3D FIB-SEM images of tumor biopsies obtained from patients with metastatic breast and pancreatic cancers. The ultrastructures, such as nuclei, nucleoli, mitochondria, endosomes, and lysosomes, are relatively better defined than their surroundings and can be segmented with high accuracy using a neural network trained with sparse manual labels. Cell segmentation, on the other hand, is much more challenging due to the lack of clear boundaries separating cells in the tissue. We adopted a multi-pronged approach combining detection, boundary propagation, and tracking for cell segmentation. Specifically, a neural network was employed to detect the intracellular space; optical flow was used to propagate cell boundaries across the z-stack from the nearest ground truth image in order to facilitate the separation of individual cells; finally, the filopodium-like protrusions were tracked to the main cells by calculating the intersection over union measure for all regions detected in consecutive images along z-stack and connecting regions with maximum overlap. The proposed cell segmentation methodology resulted in an average Dice score of 0.93. For nuclei, nucleoli, and mitochondria, the segmentation achieved Dice scores of 0.99, 0.98, and 0.86, respectively. The segmentation of FIB-SEM images will enable interpretative rendering and provide quantitative image features to be associated with relevant clinical variables.
Collapse
Affiliation(s)
- Archana Machireddy
- Program of Computer Science and Electrical Engineering, Oregon Health and Science University, Portland, OR, United States
| | - Guillaume Thibault
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, United States
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States
| | - Kevin G. Loftis
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, United States
| | - Kevin Stoltz
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, United States
| | - Cecilia E. Bueno
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, United States
| | - Hannah R. Smith
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, United States
| | - Jessica L. Riesterer
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, United States
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States
| | - Joe W. Gray
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, United States
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States
| | - Xubo Song
- Program of Computer Science and Electrical Engineering, Oregon Health and Science University, Portland, OR, United States
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, United States
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, United States
| |
Collapse
|
16
|
Thomas CI, Ryan MA, Kamasawa N, Scholl B. Postsynaptic mitochondria are positioned to support functional diversity of dendritic spines. eLife 2023; 12:RP89682. [PMID: 38059805 PMCID: PMC10703439 DOI: 10.7554/elife.89682] [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] [Indexed: 12/08/2023] Open
Abstract
Postsynaptic mitochondria are critical for the development, plasticity, and maintenance of synaptic inputs. However, their relationship to synaptic structure and functional activity is unknown. We examined a correlative dataset from ferret visual cortex with in vivo two-photon calcium imaging of dendritic spines during visual stimulation and electron microscopy reconstructions of spine ultrastructure, investigating mitochondrial abundance near functionally and structurally characterized spines. Surprisingly, we found no correlation to structural measures of synaptic strength. Instead, we found that mitochondria are positioned near spines with orientation preferences that are dissimilar to the somatic preference. Additionally, we found that mitochondria are positioned near groups of spines with heterogeneous orientation preferences. For a subset of spines with a mitochondrion in the head or neck, synapses were larger and exhibited greater selectivity to visual stimuli than those without a mitochondrion. Our data suggest mitochondria are not necessarily positioned to support the energy needs of strong spines, but rather support the structurally and functionally diverse inputs innervating the basal dendrites of cortical neurons.
Collapse
Affiliation(s)
- Connon I Thomas
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, Max Planck WayJupiterUnited States
| | - Melissa A Ryan
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, Max Planck WayJupiterUnited States
| | - Naomi Kamasawa
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, Max Planck WayJupiterUnited States
| | - Benjamin Scholl
- Department of Neuroscience, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| |
Collapse
|
17
|
Mursalimov S, Matsumoto M, Urakubo H, Deineko E, Ohno N. Unusual nuclear structures in male meiocytes of wild-type rye as revealed by volume microscopy. ANNALS OF BOTANY 2023; 132:1159-1174. [PMID: 37490684 PMCID: PMC10809220 DOI: 10.1093/aob/mcad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023]
Abstract
BACKGROUND AND AIMS During the analysis of plant male meiocytes coming from destroyed meiocyte columns (united multicellular structures formed by male meiocytes in each anther locule), a considerable amount of information becomes unavailable. Therefore, in this study intact meiocyte columns were studied by volume microscopy in wild-type rye for the most relevant presentation of 3-D structure of rye meiocytes throughout meiosis. METHODS We used two types of volume light microscopy: confocal laser scanning microscopy and non-confocal bright-field scanning microscopy combined with alcohol and aldehyde fixation, as well as serial block-face scanning electron microscopy. KEY RESULTS Unusual structures, called nuclear protuberances, were detected. At certain meiotic stages, nuclei formed protuberances that crossed the cell wall through intercellular channels and extended into the cytoplasm of neighbouring cells, while all other aspects of cell structure appeared to be normal. This phenomenon of intercellular nuclear migration (INM) was detected in most meiocytes at leptotene/zygotene. No cases of micronucleus formation or appearance of binucleated meiocytes were noticed. There were instances of direct contact between two nuclei during INM. No influence of fixation or of mechanical impact on the induction of INM was detected. CONCLUSIONS Intercellular nuclear migration in rye may be a programmed process (a normal part of rye male meiosis) or a tricky artefact that cannot be avoided in any way no matter which approach to meiocyte imaging is used. In both cases, INM seems to be an obligatory phenomenon that has previously been hidden by limitations of common microscopic techniques and by 2-D perception of plant male meiocytes. Intercellular nuclear migration cannot be ignored in any studies involving manipulations of rye anthers.
Collapse
Affiliation(s)
- Sergey Mursalimov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Institute of Postharvest and Food Sciences, Agricultural Research Organization (ARO)-Volcani Institute, Rishon LeZion, 7505101, Israel
| | - Mami Matsumoto
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
| | - Hidetoshi Urakubo
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan
- Department of Biomedical Data Science, School of Medicine, Fujita Health University, Toyoake, 470-1192, Japan
| | - Elena Deineko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, Shimotsuke, 329-0431, Japan
- Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan
| |
Collapse
|
18
|
Thomas CI, Ryan MA, McNabb MC, Kamasawa N, Scholl B. Astrocyte coverage of excitatory synapses correlates to measures of synapse structure and function in primary visual cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569664. [PMID: 38106030 PMCID: PMC10723302 DOI: 10.1101/2023.12.01.569664] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Most excitatory synapses in the mammalian brain are contacted by astrocytes, forming the tripartite synapse. This interface is thought to be critical for glutamate turnover and structural or functional dynamics of synapses. While the degree of synaptic contact of astrocytes is known to vary across brain regions and animal species, the implications of this variability remain unknown. Furthermore, precisely how astrocyte coverage of synapses relates to in vivo functional properties of individual dendritic spines has yet to be investigated. Here, we characterized perisynaptic astrocyte processes (PAPs) contacting synapses of pyramidal neurons of the ferret visual cortex and, using correlative light and electron microscopy, examined their relationship to synaptic strength and to sensory-evoked Ca2+ activity. Nearly all synapses were contacted by PAPs, and most were contacted along the axon-spine interface (ASI). Structurally, we found that the degree of PAP coverage scaled with synapse size and complexity. Functionally, we found that PAP coverage scaled with the selectivity of Ca2+ responses of individual synapses to visual stimuli and, at least for the largest synapses, scaled with the reliability of visual stimuli to evoke postsynaptic Ca2+ events. Our study shows astrocyte coverage is highly correlated with structural properties of excitatory synapses in the visual cortex and implicates astrocytes as a contributor to reliable sensory activation.
Collapse
Affiliation(s)
- Connon I Thomas
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL 33458, USA
| | - Melissa A Ryan
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL 33458, USA
- Department of Neuroscience, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Micaiah C McNabb
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL 33458, USA
- Department of Neuroscience, The Ohio State University, 460 Medical Center Drive, Columbus, OH 43210, USA
| | - Naomi Kamasawa
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL 33458, USA
| | - Benjamin Scholl
- Department of Physiology and Biophysics, University of Colorado Denver, 12800 East 19th Ave, Aurora, CO 80045, USA
| |
Collapse
|
19
|
Jadav N, Velamoor S, Huang D, Cassin L, Hazelton N, Eruera AR, Burga LN, Bostina M. Beyond the surface: Investigation of tumorsphere morphology using volume electron microscopy. J Struct Biol 2023; 215:108035. [PMID: 37805154 DOI: 10.1016/j.jsb.2023.108035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
The advent of volume electron microscopy (vEM) has provided unprecedented insights into cellular and subcellular organization, revolutionizing our understanding of cancer biology. This study presents a previously unexplored comparative analysis of the ultrastructural disparities between cancer cells cultured as monolayers and tumorspheres. By integrating a robust workflow that incorporates high-pressure freezing followed by freeze substitution (HPF/FS), serial block face scanning electron microscopy (SBF-SEM), manual and deep learning-based segmentation, and statistical analysis, we have successfully generated three-dimensional (3D) reconstructions of monolayer and tumorsphere cells, including their subcellular organelles. Our findings reveal a significant degree of variation in cellular morphology in tumorspheres. We observed the increased prevalence of nuclear envelope invaginations in tumorsphere cells compared to monolayers. Furthermore, we detected a diverse range of mitochondrial morphologies exclusively in tumorsphere cells, as well as intricate cellular interconnectivity within the tumorsphere architecture. These remarkable ultrastructural differences emphasize the use of tumorspheres as a superior model for cancer research due to their relevance to in vivo conditions. Our results strongly advocate for the utilization of tumorsphere cells in cancer research studies, enhancing the precision and relevance of experimental outcomes, and ultimately accelerating therapeutic advancements.
Collapse
Affiliation(s)
- Nickhil Jadav
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Sailakshmi Velamoor
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Daniel Huang
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Léna Cassin
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Niki Hazelton
- Otago Micro and Nano Imaging (OMNI) Electron Microscopy Suite, University of Otago, Dunedin, New Zealand
| | - Alice-Roza Eruera
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Laura N Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Otago Micro and Nano Imaging (OMNI) Electron Microscopy Suite, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
20
|
Khare H, Dongo Mendoza N, Zurzolo C. CellWalker: a user-friendly and modular computational pipeline for morphological analysis of microscopy images. Bioinformatics 2023; 39:btad710. [PMID: 38060265 PMCID: PMC10713108 DOI: 10.1093/bioinformatics/btad710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 11/07/2023] [Accepted: 12/06/2023] [Indexed: 12/08/2023] Open
Abstract
SUMMARY The implementation of computational tools for analysis of microscopy images has been one of the most important technological innovations in biology, providing researchers unmatched capabilities to comprehend cell shape and connectivity. While numerous tools exist for image annotation and segmentation, there is a noticeable gap when it comes to morphometric analysis of microscopy images. Most existing tools often measure features solely on 2D serial images, which can be difficult to extrapolate to 3D. For this reason, we introduce CellWalker, a computational toolbox that runs inside Blender, an open-source computer graphics software. This add-on improves the morphological analysis by seamlessly integrating analysis tools into the Blender workflow, providing visual feedback through a powerful 3D visualization, and leveraging the resources of Blender's community. CellWalker provides several morphometric analysis tools that can be used to calculate distances, volume, surface areas and to determine cross-sectional properties. It also includes tools to build skeletons, calculate distributions of subcellular organelles. In addition, this python-based tool contains 'visible-source' IPython notebooks accessories for segmentation of 2D/3D microscopy images using deep learning and visualization of the segmented images that are required as input to CellWalker. Overall, CellWalker provides practical tools for segmentation and morphological analysis of microscopy images in the form of an open-source and modular pipeline which allows a complete access to fine-tuning of algorithms through visible-source code while still retaining a result-oriented interface. AVAILABILITY AND IMPLEMENTATION CellWalker source code is available on GitHub (https://github.com/utraf-pasteur-institute/Cellwalker-blender and https://github.com/utraf-pasteur-institute/Cellwalker-notebooks) under a GPL-3 license.
Collapse
Affiliation(s)
- Harshavardhan Khare
- Membrane Traffic and Pathogenesis Unit, Department of Cell Biology and Infection, CNRS UMR 3691, Université de Paris, Institut Pasteur, Paris, 75015, France
| | - Nathaly Dongo Mendoza
- Membrane Traffic and Pathogenesis Unit, Department of Cell Biology and Infection, CNRS UMR 3691, Université de Paris, Institut Pasteur, Paris, 75015, France
- Centro de Investigación en Bioingeniería – BIO, Universidad de Ingeniería y Tecnología – UTEC, Lima, 15063, Perú
| | - Chiara Zurzolo
- Membrane Traffic and Pathogenesis Unit, Department of Cell Biology and Infection, CNRS UMR 3691, Université de Paris, Institut Pasteur, Paris, 75015, France
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, 80131, Italy
| |
Collapse
|
21
|
Ebner M, Puchkov D, López-Ortega O, Muthukottiappan P, Su Y, Schmied C, Zillmann S, Nikonenko I, Koddebusch J, Dornan GL, Lucht MT, Koka V, Jang W, Koch PA, Wallroth A, Lehmann M, Brügger B, Pende M, Winter D, Haucke V. Nutrient-regulated control of lysosome function by signaling lipid conversion. Cell 2023; 186:5328-5346.e26. [PMID: 37883971 DOI: 10.1016/j.cell.2023.09.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 08/04/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
Lysosomes serve dual antagonistic functions in cells by mediating anabolic growth signaling and the catabolic turnover of macromolecules. How these janus-faced activities are regulated in response to cellular nutrient status is poorly understood. We show here that lysosome morphology and function are reversibly controlled by a nutrient-regulated signaling lipid switch that triggers the conversion between peripheral motile mTOR complex 1 (mTORC1) signaling-active and static mTORC1-inactive degradative lysosomes clustered at the cell center. Starvation-triggered relocalization of phosphatidylinositol 4-phosphate (PI(4)P)-metabolizing enzymes reshapes the lysosomal surface proteome to facilitate lysosomal proteolysis and to repress mTORC1 signaling. Concomitantly, lysosomal phosphatidylinositol 3-phosphate (PI(3)P), which marks motile signaling-active lysosomes in the cell periphery, is erased. Interference with this PI(3)P/PI(4)P lipid switch module impairs the adaptive response of cells to altering nutrient supply. Our data unravel a key function for lysosomal phosphoinositide metabolism in rewiring organellar membrane dynamics in response to cellular nutrient status.
Collapse
Affiliation(s)
- Michael Ebner
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Dmytro Puchkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Orestes López-Ortega
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Paris, France
| | - Pathma Muthukottiappan
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, 53115 Bonn, Germany
| | - Yanwei Su
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Christopher Schmied
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Silke Zillmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Iryna Nikonenko
- Department of Basic Neurosciences and the Center for Neuroscience, CMU, University of Geneva, 1211 Geneva 4, Switzerland
| | - Jochen Koddebusch
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Gillian L Dornan
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Max T Lucht
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Vonda Koka
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Paris, France
| | - Wonyul Jang
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | | | - Alexander Wallroth
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Mario Pende
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Paris, France
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, 53115 Bonn, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany; Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| |
Collapse
|
22
|
Tetenborg S, Liss V, Breitsprecher L, Timonina K, Kotova A, Acevedo Harnecker AJ, Yuan C, Shihabeddin E, Ariakia F, Qin G, Chengzhi C, Dedek K, Zoidl G, Hensel M, O'Brien J. Intralumenal docking of connexin 36 channels in the ER isolates mistrafficked protein. J Biol Chem 2023; 299:105282. [PMID: 37742923 PMCID: PMC10637963 DOI: 10.1016/j.jbc.2023.105282] [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] [Received: 03/11/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/26/2023] Open
Abstract
The intracellular domains of connexins are essential for the assembly of gap junctions. For connexin 36 (Cx36), the major neuronal connexin, it has been shown that a dysfunctional PDZ-binding motif interferes with electrical synapse formation. However, it is still unknown how this motif coordinates the transport of Cx36. In the present study, we characterize a phenotype of Cx36 mutants that lack a functional PDZ-binding motif using HEK293T cells as an expression system. We provide evidence that an intact PDZ-binding motif is critical for proper endoplasmic reticulum (ER) export of Cx36. Removing the PDZ-binding motif of Cx36 results in ER retention and the formation of multimembrane vesicles containing gap junction-like connexin aggregates. Using a combination of site-directed mutagenesis and electron micrographs, we reveal that these vesicles consist of Cx36 channels that docked prematurely in the ER. Our data suggest a model in which ER-retained Cx36 channels reshape the ER membrane into concentric whorls that are released into the cytoplasm.
Collapse
Affiliation(s)
| | - Viktoria Liss
- Department of Biology/Chemistry, iBiOs-Integrated Bioimaging Facility, CellNanOs - Center of Cellular Nanoanalytics, Osnabrück, Germany; Department of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Leonhard Breitsprecher
- Department of Biology/Chemistry, iBiOs-Integrated Bioimaging Facility, CellNanOs - Center of Cellular Nanoanalytics, Osnabrück, Germany; Department of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Ksenia Timonina
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Anna Kotova
- Department of Biology, York University, Toronto, Ontario, Canada
| | | | - Chunxu Yuan
- Animal Navigation/Neurosensorics, Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Eyad Shihabeddin
- College of Optometry, University of Houston, Houston, Texas, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Fatemeh Ariakia
- College of Optometry, University of Houston, Houston, Texas, USA
| | - Guoting Qin
- College of Optometry, University of Houston, Houston, Texas, USA
| | - Cai Chengzhi
- Department of Chemistry, University of Houston, Houston, Texas, USA
| | - Karin Dedek
- Animal Navigation/Neurosensorics, Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany; Research Center Neurosensory Science, University of Oldenburg, Oldenburg, Germany
| | - Georg Zoidl
- Department of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Department of Biology/Chemistry, iBiOs-Integrated Bioimaging Facility, CellNanOs - Center of Cellular Nanoanalytics, Osnabrück, Germany; Department of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - John O'Brien
- College of Optometry, University of Houston, Houston, Texas, USA.
| |
Collapse
|
23
|
Anand A, Mazur AC, Rosell-Arevalo P, Franzkoch R, Breitsprecher L, Listian SA, Hüttel SV, Müller D, Schäfer DG, Vormittag S, Hilbi H, Maniak M, Gutierrez MG, Barisch C. ER-dependent membrane repair of mycobacteria-induced vacuole damage. mBio 2023; 14:e0094323. [PMID: 37676004 PMCID: PMC10653851 DOI: 10.1128/mbio.00943-23] [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] [Received: 04/14/2023] [Accepted: 07/13/2023] [Indexed: 09/08/2023] Open
Abstract
IMPORTANCE Tuberculosis still remains a global burden and is one of the top infectious diseases from a single pathogen. Mycobacterium tuberculosis, the causative agent, has perfected many ways to replicate and persist within its host. While mycobacteria induce vacuole damage to evade the toxic environment and eventually escape into the cytosol, the host recruits repair machineries to restore the MCV membrane. However, how lipids are delivered for membrane repair is poorly understood. Using advanced fluorescence imaging and volumetric correlative approaches, we demonstrate that this involves the recruitment of the endoplasmic reticulum (ER)-Golgi lipid transfer protein OSBP8 in the Dictyostelium discoideum/Mycobacterium marinum system. Strikingly, depletion of OSBP8 affects lysosomal function accelerating mycobacterial growth. This indicates that an ER-dependent repair pathway constitutes a host defense mechanism against intracellular pathogens such as M. tuberculosis.
Collapse
Affiliation(s)
- Aby Anand
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Anna-Carina Mazur
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Patricia Rosell-Arevalo
- Host–Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Rico Franzkoch
- Integrated Bioimaging Facility, Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Leonhard Breitsprecher
- Integrated Bioimaging Facility, Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Stevanus A. Listian
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Sylvana V. Hüttel
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Danica Müller
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Deise G. Schäfer
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Simone Vormittag
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zürich, Zürich, Switzerland
| | - Markus Maniak
- Department of Cell Biology, University of Kassel, Kassel, Germany
| | - Maximiliano G. Gutierrez
- Host–Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Caroline Barisch
- Division of Molecular Infection Biology, Department of Biology & Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Division of Host-Microbe Interactome, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| |
Collapse
|
24
|
Pispa J, Mikkonen E, Arpalahti L, Jin C, Martínez-Fernández C, Cerón J, Holmberg CI. AKIR-1 regulates proteasome subcellular function in Caenorhabditis elegans. iScience 2023; 26:107886. [PMID: 37767001 PMCID: PMC10520889 DOI: 10.1016/j.isci.2023.107886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 07/07/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Polyubiquitinated proteins are primarily degraded by the ubiquitin-proteasome system (UPS). Proteasomes are present both in the cytoplasm and nucleus. Here, we investigated mechanisms coordinating proteasome subcellular localization and activity in a multicellular organism. We identified the nuclear protein-encoding gene akir-1 as a proteasome regulator in a genome-wide Caenorhabditis elegans RNAi screen. We demonstrate that depletion of akir-1 causes nuclear accumulation of endogenous polyubiquitinated proteins in intestinal cells, concomitant with slower in vivo proteasomal degradation in this subcellular compartment. Remarkably, akir-1 is essential for nuclear localization of proteasomes both in oocytes and intestinal cells but affects differentially the subcellular distribution of polyubiquitinated proteins. We further reveal that importin ima-3 genetically interacts with akir-1 and influences nuclear localization of a polyubiquitin-binding reporter. Our study shows that the conserved AKIR-1 is an important regulator of the subcellular function of proteasomes in a multicellular organism, suggesting a role for AKIR-1 in proteostasis maintenance.
Collapse
Affiliation(s)
- Johanna Pispa
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Elisa Mikkonen
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Leena Arpalahti
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Congyu Jin
- Department of Anatomy, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Carmen Martínez-Fernández
- Modeling Human Diseases in C. elegans Group, Genes, Diseases, and Therapies Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Julián Cerón
- Modeling Human Diseases in C. elegans Group, Genes, Diseases, and Therapies Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Carina I. Holmberg
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| |
Collapse
|
25
|
Rizalar FS, Lucht MT, Petzoldt A, Kong S, Sun J, Vines JH, Telugu NS, Diecke S, Kaas T, Bullmann T, Schmied C, Löwe D, King JS, Cho W, Hallermann S, Puchkov D, Sigrist SJ, Haucke V. Phosphatidylinositol 3,5-bisphosphate facilitates axonal vesicle transport and presynapse assembly. Science 2023; 382:223-230. [PMID: 37824668 PMCID: PMC10938084 DOI: 10.1126/science.adg1075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 08/16/2023] [Indexed: 10/14/2023]
Abstract
Neurons relay information via specialized presynaptic compartments for neurotransmission. Unlike conventional organelles, the specialized apparatus characterizing the neuronal presynapse must form de novo. How the components for presynaptic neurotransmission are transported and assembled is poorly understood. Our results show that the rare late endosomal signaling lipid phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2] directs the axonal cotransport of synaptic vesicle and active zone proteins in precursor vesicles in human neurons. Precursor vesicles are distinct from conventional secretory organelles, endosomes, and degradative lysosomes and are transported by coincident detection of PI(3,5)P2 and active ARL8 via kinesin KIF1A to the presynaptic compartment. Our findings identify a crucial mechanism that mediates the delivery of synaptic vesicle and active zone proteins to developing synapses.
Collapse
Affiliation(s)
- Filiz Sila Rizalar
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Max T. Lucht
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Astrid Petzoldt
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Shuhan Kong
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Jiachen Sun
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - James H. Vines
- School of Biosciences, University of Sheffield, Firth Court Western Bank, Sheffield S10 2TN, UK
| | - Narasimha Swamy Telugu
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Technology Platform Pluripotent Stem Cells, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Sebastian Diecke
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Technology Platform Pluripotent Stem Cells, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Thomas Kaas
- Leipzig University, Carl-Ludwig-Institute of Physiology, Faculty of Medicine, 04103 Leipzig, Germany
| | - Torsten Bullmann
- Leipzig University, Carl-Ludwig-Institute of Physiology, Faculty of Medicine, 04103 Leipzig, Germany
| | - Christopher Schmied
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Delia Löwe
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Jason S. King
- School of Biosciences, University of Sheffield, Firth Court Western Bank, Sheffield S10 2TN, UK
| | - Wonhwa Cho
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Stefan Hallermann
- Leipzig University, Carl-Ludwig-Institute of Physiology, Faculty of Medicine, 04103 Leipzig, Germany
| | - Dmytro Puchkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Stephan J. Sigrist
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
- Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| |
Collapse
|
26
|
Thomas CI, Ryan MA, Kamasawa N, Scholl B. Postsynaptic mitochondria are positioned to support functional diversity of dendritic spines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549063. [PMID: 37502969 PMCID: PMC10370038 DOI: 10.1101/2023.07.14.549063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Postsynaptic mitochondria are critical to the development, plasticity, and maintenance of synaptic inputs. However, their relationship to synaptic structure and functional activity is unknown. We examined a correlative dataset from ferret visual cortex with in vivo two-photon calcium imaging of dendritic spines during visual stimulation and electron microscopy (EM) reconstructions of spine ultrastructure, investigating mitochondrial abundance near functionally- and structurally-characterized spines. Surprisingly, we found no correlation to structural measures of synaptic strength. Instead, we found that mitochondria are positioned near spines with orientation preferences that are dissimilar to the somatic preference. Additionally, we found that mitochondria are positioned near groups of spines with heterogeneous orientation preferences. For a subset of spines with mitochondrion in the head or neck, synapses were larger and exhibited greater selectivity to visual stimuli than those without a mitochondrion. Our data suggest mitochondria are not necessarily positioned to support the energy needs of strong spines, but rather support the structurally and functionally diverse inputs innervating the basal dendrites of cortical neurons.
Collapse
Affiliation(s)
- Connon I. Thomas
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL 33458, USA
| | - Melissa A. Ryan
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL 33458, USA
- Present Address: Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Naomi Kamasawa
- Electron Microscopy Core Facility, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL 33458, USA
| | - Benjamin Scholl
- Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA, 19104, USA
| |
Collapse
|
27
|
Bjerke IE, Yates SC, Carey H, Bjaalie JG, Leergaard TB. Scaling up cell-counting efforts in neuroscience through semi-automated methods. iScience 2023; 26:107562. [PMID: 37636060 PMCID: PMC10457595 DOI: 10.1016/j.isci.2023.107562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
Quantifying how the cellular composition of brain regions vary across development, aging, sex, and disease, is crucial in experimental neuroscience, and the accuracy of different counting methods is continuously debated. Due to the tedious nature of most counting procedures, studies are often restricted to one or a few brain regions. Recently, there have been considerable methodological advances in combining semi-automated feature extraction with brain atlases for cell quantification. Such methods hold great promise for scaling up cell-counting efforts. However, little focus has been paid to how these methods should be implemented and reported to support reproducibility. Here, we provide an overview of practices for conducting and reporting cell counting in mouse and rat brains, showing that critical details for interpretation are typically lacking. We go on to discuss how novel methods may increase efficiency and reproducibility of cell counting studies. Lastly, we provide practical recommendations for researchers planning cell counting.
Collapse
Affiliation(s)
- Ingvild Elise Bjerke
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Sharon Christine Yates
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Harry Carey
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan Gunnar Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve Brauns Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| |
Collapse
|
28
|
Nomura M, Ohta K, Nishigami Y, Nakayama T, Nakamura KI, Tadakuma K, Galipon J. Three-dimensional architecture and assembly mechanism of the egg-shaped shell in testate amoeba Paulinella micropora. Front Cell Dev Biol 2023; 11:1232685. [PMID: 37731817 PMCID: PMC10507277 DOI: 10.3389/fcell.2023.1232685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023] Open
Abstract
Unicellular euglyphid testate amoeba Paulinella micropora with filose pseudopodia secrete approximately 50 siliceous scales into the extracellular template-free space to construct a shell isomorphic to that of its mother cell. This shell-constructing behavior is analogous to building a house with bricks, and a complex mechanism is expected to be involved for a single-celled amoeba to achieve such a phenomenon; however, the three-dimensional (3D) structure of the shell and its assembly in P. micropora are still unknown. In this study, we aimed to clarify the positional relationship between the cytoplasmic and extracellular scales and the structure of the egg-shaped shell in P. micropora during shell construction using focused ion beam scanning electron microscopy (FIB-SEM). 3D reconstruction revealed an extensive invasion of the electron-dense cytoplasm between the long sides of the positioned and stacked scales, which was predicted to be mediated by actin filament extension. To investigate the architecture of the shell of P. micropora, each scale was individually segmented, and the position of its centroid was plotted. The scales were arranged in a left-handed, single-circular ellipse in a twisted arrangement. In addition, we 3D printed individual scales and assembled them, revealing new features of the shell assembly mechanism of P. micropora. Our results indicate that the shell of P. micropora forms an egg shape by the regular stacking of precisely designed scales, and that the cytoskeleton is involved in the construction process.
Collapse
Affiliation(s)
- Mami Nomura
- Faculty of Science, Yamagata University, Yamagata, Japan
| | - Keisuke Ohta
- Division of Microscopic and Developmental Anatomy, Department of Anatomy, Kurume University School of Medicine, Kurume, Japan
- Advanced Imaging Research Center, Kurume University School of Medicine, Kurume, Japan
| | - Yukinori Nishigami
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Research Institute for Electronic Science, Hokkaido University, Sapporo, Japan
| | - Takuro Nakayama
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kei-Ichiro Nakamura
- Division of Microscopic and Developmental Anatomy, Department of Anatomy, Kurume University School of Medicine, Kurume, Japan
- Advanced Imaging Research Center, Kurume University School of Medicine, Kurume, Japan
| | - Kenjiro Tadakuma
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Tough Cyberphysical AI Research Center, Tohoku University, Sendai, Japan
| | - Josephine Galipon
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Institute for Advanced Sciences, Keio University, Tsuruoka, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Graduate School of Science and Engineering, Yamagata University, Yonezawa, Japan
| |
Collapse
|
29
|
Konopová B, Týč J. Minimal resin embedding of SBF-SEM samples reduces charging and facilitates finding a surface-linked region of interest. Front Zool 2023; 20:29. [PMID: 37641135 PMCID: PMC10463905 DOI: 10.1186/s12983-023-00507-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/02/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND For decoding the mechanism of how cells and organs function information on their ultrastructure is essential. High-resolution 3D imaging has revolutionized morphology. Serial block face scanning electron microscopy (SBF-SEM) offers non-laborious, automated imaging in 3D of up to ~ 1 mm3 large biological objects at nanometer-scale resolution. For many samples there are obstacles. Quality imaging is often hampered by charging effects, which originate in the nonconductive resin used for embedding. Especially, if the imaged region of interest (ROI) includes the surface of the sample and neighbours the empty resin, which insulates the object. This extra resin also obscures the sample's morphology, thus making navigation to the ROI difficult. RESULTS Using the example of small arthropods and a fish roe we describe a workflow to prepare samples for SBF-SEM using the minimal resin (MR) embedding method. We show that for imaging of surface structures this simple approach conveniently tackles and solves both of the two major problems-charging and ROI localization-that complicate imaging of SBF-SEM samples embedded in an excess of overlying resin. As the surface ROI is not masked by the resin, samples can be precisely trimmed before they are placed into the imaging chamber. The initial approaching step is fast and easy. No extra trimming inside the microscope is necessary. Importantly, charging is absent or greatly reduced meaning that imaging can be accomplished under good vacuum conditions, typically at the optimal high vacuum. This leads to better resolution, better signal to noise ratio, and faster image acquisition. CONCLUSIONS In MR embedded samples charging is minimized and ROI easily targeted. MR embedding does not require any special equipment or skills. It saves effort, microscope time and eventually leads to high quality data. Studies on surface-linked ROIs, or any samples normally surrounded by the excess of resin, would benefit from adopting the technique.
Collapse
Affiliation(s)
- Barbora Konopová
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic.
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | - Jiří Týč
- Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic.
| |
Collapse
|
30
|
Kolotuev I. Work smart, not hard: How array tomography can help increase the ultrastructure data output. J Microsc 2023. [PMID: 37626455 DOI: 10.1111/jmi.13217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
Transmission electron microscopy has been essential for understanding cell biology for over six decades. Volume electron microscopy tools, such as serial block face and focused ion beam scanning electron microscopy acquisition, brought a new era to ultrastructure analysis. 'Array Tomography' (AT) refers to sequential image acquisition of resin-embedded sample sections on a large support (coverslip, glass slide, silicon wafers) for immunolabelling with multiple fluorescent labels, occasionally combined with ultrastructure observation. Subsequently, the term was applied to generating and imaging a series of sections to acquire a 3D representation of a structure using scanning electron microscopy (SEM). Although this is a valuable application, the potential of AT is to facilitate many tasks that are difficult or even impossible to obtain by Transmission Electron Microscopy (TEM). Due to the straightforward nature and versatility of AT sample preparation and image acquisition, the technique can be applied practically to any biological sample for selected sections or volume electron microscopy analysis. Furthermore, in addition to the benefits described here, AT is compatible with morphological analysis, multiplex immunolabelling, immune-gold labelling, and correlative light and electron microscopy workflow applicable for single cells, tissue and small organisms. This versatility makes AT attractive not only for basic research but as a diagnostic tool with a simplified routine.
Collapse
Affiliation(s)
- Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
31
|
Mocaer K, Mizzon G, Gunkel M, Halavatyi A, Steyer A, Oorschot V, Schorb M, Le Kieffre C, Yee DP, Chevalier F, Gallet B, Decelle J, Schwab Y, Ronchi P. Targeted volume correlative light and electron microscopy of an environmental marine microorganism. J Cell Sci 2023; 136:jcs261355. [PMID: 37455654 PMCID: PMC10445747 DOI: 10.1242/jcs.261355] [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] [Received: 05/22/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Photosynthetic microalgae are responsible for an important fraction of CO2 fixation and O2 production on Earth. Three-dimensional (3D) ultrastructural characterization of these organisms in their natural environment can contribute to a deeper understanding of their cell biology. However, the low throughput of volume electron microscopy (vEM) methods along with the complexity and heterogeneity of environmental samples pose great technical challenges. In the present study, we used a workflow based on a specific electron microscopy sample preparation method compatible with both light and vEM imaging in order to target one cell among a complex natural community. This method revealed the 3D subcellular landscape of a photosynthetic dinoflagellate, which we identified as Ensiculifera tyrrhenica, with quantitative characterization of multiple organelles. We show that this cell contains a single convoluted chloroplast and show the arrangement of the flagellar apparatus with its associated photosensitive elements. Moreover, we observed partial chromatin unfolding, potentially associated with transcription activity in these organisms, in which chromosomes are permanently condensed. Together with providing insights in dinoflagellate biology, this proof-of-principle study illustrates an efficient tool for the targeted ultrastructural analysis of environmental microorganisms in heterogeneous mixes.
Collapse
Affiliation(s)
- Karel Mocaer
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between the European Molecular Biology Laboratory and the Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Giulia Mizzon
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, CIID, 69120 Heidelberg, Germany
- German Center for Infection Research, Heidelberg partner site, 69120 Heidelberg, Germany
| | - Manuel Gunkel
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Aliaksandr Halavatyi
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Anna Steyer
- EMBL Imaging Centre, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Viola Oorschot
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Martin Schorb
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Daniel P. Yee
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38054 Grenoble, France
| | - Fabien Chevalier
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38054 Grenoble, France
| | - Benoit Gallet
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France
| | - Johan Decelle
- Université Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, 38054 Grenoble, France
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| |
Collapse
|
32
|
Wang L, Goldwag J, Bouyea M, Barra J, Matteson K, Maharjan N, Eladdadi A, Embrechts MJ, Intes X, Kruger U, Barroso M. Spatial topology of organelle is a new breast cancer cell classifier. iScience 2023; 26:107229. [PMID: 37519903 PMCID: PMC10384275 DOI: 10.1016/j.isci.2023.107229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 05/10/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023] Open
Abstract
Genomics and proteomics have been central to identify tumor cell populations, but more accurate approaches to classify cell subtypes are still lacking. We propose a new methodology to accurately classify cancer cells based on their organelle spatial topology. Herein, we developed an organelle topology-based cell classification pipeline (OTCCP), which integrates artificial intelligence (AI) and imaging quantification to analyze organelle spatial distribution and inter-organelle topology. OTCCP was used to classify a panel of human breast cancer cells, grown as 2D monolayer or 3D tumor spheroids using early endosomes, mitochondria, and their inter-organelle contacts. Organelle topology allows for a highly precise differentiation between cell lines of different subtypes and aggressiveness. These findings lay the groundwork for using organelle topological profiling as a fast and efficient method for phenotyping breast cancer function as well as a discovery tool to advance our understanding of cancer cell biology at the subcellular level.
Collapse
Affiliation(s)
- Ling Wang
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Joshua Goldwag
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Megan Bouyea
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Jonathan Barra
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Kailie Matteson
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Niva Maharjan
- Department of Mathematics, The College of Saint Rose, Albany, NY 12203, USA
| | - Amina Eladdadi
- Department of Mathematics, The College of Saint Rose, Albany, NY 12203, USA
| | - Mark J. Embrechts
- Department of Industrial and Systems Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Uwe Kruger
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| |
Collapse
|
33
|
Adams RA, Liu Z, Hsieh C, Marko M, Lederer WJ, Jafri MS, Mannella C. Structural Analysis of Mitochondria in Cardiomyocytes: Insights into Bioenergetics and Membrane Remodeling. Curr Issues Mol Biol 2023; 45:6097-6115. [PMID: 37504301 PMCID: PMC10378267 DOI: 10.3390/cimb45070385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023] Open
Abstract
Mitochondria in mammalian cardiomyocytes display considerable structural heterogeneity, the significance of which is not currently understood. We use electron microscopic tomography to analyze a dataset of 68 mitochondrial subvolumes to look for correlations among mitochondrial size and shape, crista morphology and membrane density, and organelle location within rat cardiac myocytes. A tomographic analysis guided the definition of four classes of crista morphology: lamellar, tubular, mixed and transitional, the last associated with remodeling between lamellar and tubular cristae. Correlations include an apparent bias for mitochondria with lamellar cristae to be located in the regions between myofibrils and a two-fold larger crista membrane density in mitochondria with lamellar cristae relative to mitochondria with tubular cristae. The examination of individual cristae inside mitochondria reveals local variations in crista topology, such as extent of branching, alignment of fenestrations and progressive changes in membrane morphology and packing density. The findings suggest both a rationale for the interfibrillar location of lamellar mitochondria and a pathway for crista remodeling from lamellar to tubular morphology.
Collapse
Affiliation(s)
- Raquel A. Adams
- Krasnow Institute for Advanced Study and School of Systems Biology, George Mason University, Fairfax, VA 22030, USA;
| | - Zheng Liu
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA (M.M.)
| | - Chongere Hsieh
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA (M.M.)
| | - Michael Marko
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA (M.M.)
| | - W. Jonathan Lederer
- Department of Physiology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA;
- Center for Biomedical Engineering and Technology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - M. Saleet Jafri
- Krasnow Institute for Advanced Study and School of Systems Biology, George Mason University, Fairfax, VA 22030, USA;
- Center for Biomedical Engineering and Technology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Carmen Mannella
- Department of Physiology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA;
- Center for Biomedical Engineering and Technology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| |
Collapse
|
34
|
Ferrandiz N, Royle SJ. 3D Ultrastructural Visualization of Mitosis Fidelity in Human Cells Using Serial Block Face Scanning Electron Microscopy (SBF-SEM). Bio Protoc 2023; 13:e4708. [PMID: 37449034 PMCID: PMC10336565 DOI: 10.21769/bioprotoc.4708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/01/2023] [Accepted: 04/19/2023] [Indexed: 07/18/2023] Open
Abstract
Errors in chromosome segregation during mitosis lead to chromosome instability, resulting in an unbalanced number of chromosomes in the daughter cells. Light microscopy has been used extensively to study chromosome missegregation by visualizing errors of the mitotic spindle. However, less attention has been paid to understanding spindle function in the broader context of intracellular structures and organelles during mitosis. Here, we outline a protocol to visualize chromosomes and endomembranes in mitosis, combining light microscopy and 3D volume electron microscopy, serial block-face scanning electron microscopy (SBF-SEM). SBF-SEM provides high-resolution imaging of large volumes and subcellular structures, followed by image analysis and 3D reconstruction. This protocol allows scientists to visualize the whole subcellular context of the spindle during mitosis.
Collapse
Affiliation(s)
- Nuria Ferrandiz
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Stephen J. Royle
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| |
Collapse
|
35
|
Schäffner E, Bosch-Queralt M, Edgar JM, Lehning M, Strauß J, Fleischer N, Kungl T, Wieghofer P, Berghoff SA, Reinert T, Krueger M, Morawski M, Möbius W, Barrantes-Freer A, Stieler J, Sun T, Saher G, Schwab MH, Wrede C, Frosch M, Prinz M, Reich DS, Flügel A, Stadelmann C, Fledrich R, Nave KA, Stassart RM. Myelin insulation as a risk factor for axonal degeneration in autoimmune demyelinating disease. Nat Neurosci 2023; 26:1218-1228. [PMID: 37386131 PMCID: PMC10322724 DOI: 10.1038/s41593-023-01366-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/17/2023] [Indexed: 07/01/2023]
Abstract
Axonal degeneration determines the clinical outcome of multiple sclerosis and is thought to result from exposure of denuded axons to immune-mediated damage. Therefore, myelin is widely considered to be a protective structure for axons in multiple sclerosis. Myelinated axons also depend on oligodendrocytes, which provide metabolic and structural support to the axonal compartment. Given that axonal pathology in multiple sclerosis is already visible at early disease stages, before overt demyelination, we reasoned that autoimmune inflammation may disrupt oligodendroglial support mechanisms and hence primarily affect axons insulated by myelin. Here, we studied axonal pathology as a function of myelination in human multiple sclerosis and mouse models of autoimmune encephalomyelitis with genetically altered myelination. We demonstrate that myelin ensheathment itself becomes detrimental for axonal survival and increases the risk of axons degenerating in an autoimmune environment. This challenges the view of myelin as a solely protective structure and suggests that axonal dependence on oligodendroglial support can become fatal when myelin is under inflammatory attack.
Collapse
Affiliation(s)
- Erik Schäffner
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Paul Flechsig Institute of Neuropathology, University Clinic Leipzig, Leipzig, Germany
| | - Mar Bosch-Queralt
- Paul Flechsig Institute of Neuropathology, University Clinic Leipzig, Leipzig, Germany
| | - Julia M Edgar
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Maria Lehning
- Paul Flechsig Institute of Neuropathology, University Clinic Leipzig, Leipzig, Germany
| | - Judith Strauß
- Institute of Neuroimmunology and Multiple Sclerosis Research, University Medical Center Göttingen, Göttingen, Germany
| | - Niko Fleischer
- Paul Flechsig Institute of Neuropathology, University Clinic Leipzig, Leipzig, Germany
| | - Theresa Kungl
- Institute of Anatomy, Leipzig University, Leipzig, Germany
| | - Peter Wieghofer
- Institute of Anatomy, Leipzig University, Leipzig, Germany
- Cellular Neuroanatomy, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Stefan A Berghoff
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Tilo Reinert
- Paul Flechsig Institute of Neuropathology, University Clinic Leipzig, Leipzig, Germany
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Martin Krueger
- Institute of Anatomy, Leipzig University, Leipzig, Germany
| | - Markus Morawski
- Paul Flechsig Institute of Brain Research, Leipzig University, Leipzig, Germany
| | - Wiebke Möbius
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | | | - Jens Stieler
- Paul Flechsig Institute of Brain Research, Leipzig University, Leipzig, Germany
| | - Ting Sun
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Gesine Saher
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Markus H Schwab
- Paul Flechsig Institute of Neuropathology, University Clinic Leipzig, Leipzig, Germany
| | - Christoph Wrede
- Institute of Functional and Applied Anatomy, Research Core Unit Electron Microscopy, Hannover Medical School, Hannover, Germany
| | - Maximilian Frosch
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Marco Prinz
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
- Centre for NeuroModulation (NeuroModBasics), University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Alexander Flügel
- Institute of Neuroimmunology and Multiple Sclerosis Research, University Medical Center Göttingen, Göttingen, Germany
| | - Christine Stadelmann
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
| | - Robert Fledrich
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Institute of Anatomy, Leipzig University, Leipzig, Germany.
| | - Klaus-Armin Nave
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Ruth M Stassart
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Paul Flechsig Institute of Neuropathology, University Clinic Leipzig, Leipzig, Germany.
| |
Collapse
|
36
|
Kucińska MK, Fedry J, Galli C, Morone D, Raimondi A, Soldà T, Förster F, Molinari M. TMX4-driven LINC complex disassembly and asymmetric autophagy of the nuclear envelope upon acute ER stress. Nat Commun 2023; 14:3497. [PMID: 37311770 DOI: 10.1038/s41467-023-39172-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/31/2023] [Indexed: 06/15/2023] Open
Abstract
The endoplasmic reticulum (ER) is an organelle of nucleated cells that produces proteins, lipids and oligosaccharides. ER volume and activity are increased upon induction of unfolded protein responses (UPR) and are reduced upon activation of ER-phagy programs. A specialized domain of the ER, the nuclear envelope (NE), protects the cell genome with two juxtaposed lipid bilayers, the inner and outer nuclear membranes (INM and ONM) separated by the perinuclear space (PNS). Here we report that expansion of the mammalian ER upon homeostatic perturbations results in TMX4 reductase-driven disassembly of the LINC complexes connecting INM and ONM and in ONM swelling. The physiologic distance between ONM and INM is restored, upon resolution of the ER stress, by asymmetric autophagy of the NE, which involves the LC3 lipidation machinery, the autophagy receptor SEC62 and the direct capture of ONM-derived vesicles by degradative LAMP1/RAB7-positive endolysosomes in a catabolic pathway mechanistically defined as micro-ONM-phagy.
Collapse
Affiliation(s)
- Marika K Kucińska
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500, Bellinzona, Switzerland
- Department of Biology, Swiss Federal Institute of Technology, CH-8093, Zurich, Switzerland
| | - Juliette Fedry
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Carmela Galli
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500, Bellinzona, Switzerland
| | - Diego Morone
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500, Bellinzona, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3000, Bern, Switzerland
| | - Andrea Raimondi
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500, Bellinzona, Switzerland
- Experimental Imaging Center, San Raffaele Scientific Institute, I-20132, Milan, Italy
| | - Tatiana Soldà
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500, Bellinzona, Switzerland
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Maurizio Molinari
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500, Bellinzona, Switzerland.
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
| |
Collapse
|
37
|
Bharathan NK, Giang W, Hoffman CL, Aaron JS, Khuon S, Chew TL, Preibisch S, Trautman ET, Heinrich L, Bogovic J, Bennett D, Ackerman D, Park W, Petruncio A, Weigel AV, Saalfeld S, Wayne Vogl A, Stahley SN, Kowalczyk AP. Architecture and dynamics of a desmosome-endoplasmic reticulum complex. Nat Cell Biol 2023; 25:823-835. [PMID: 37291267 PMCID: PMC10960982 DOI: 10.1038/s41556-023-01154-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 04/24/2023] [Indexed: 06/10/2023]
Abstract
The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signalling and lipid transfer. Here, using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometre proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization, mobility and expression of ER stress transcripts. These findings indicate that desmosomes and the keratin cytoskeleton regulate the distribution, function and dynamics of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction.
Collapse
Affiliation(s)
- Navaneetha Krishnan Bharathan
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - William Giang
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Coryn L Hoffman
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jesse S Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Satya Khuon
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Stephan Preibisch
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Eric T Trautman
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Larissa Heinrich
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - John Bogovic
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Davis Bennett
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - David Ackerman
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Woohyun Park
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Alyson Petruncio
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Aubrey V Weigel
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Stephan Saalfeld
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - A Wayne Vogl
- Life Sciences Institute and the Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sara N Stahley
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Andrew P Kowalczyk
- Departments of Dermatology and Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| |
Collapse
|
38
|
Malik H, Idris AS, Toha SF, Mohd Idris I, Daud MF, Azmi NL. A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations. PeerJ Comput Sci 2023; 9:e1364. [PMID: 37346656 PMCID: PMC10280419 DOI: 10.7717/peerj-cs.1364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/04/2023] [Indexed: 06/23/2023]
Abstract
Cell culture is undeniably important for multiple scientific applications, including pharmaceuticals, transplants, and cosmetics. However, cell culture involves multiple manual steps, such as regularly analyzing cell images for their health and morphology. Computer scientists have developed algorithms to automate cell imaging analysis, but they are not widely adopted by biologists, especially those lacking an interactive platform. To address the issue, we compile and review existing open-source cell image processing tools that provide interactive interfaces for management and prediction tasks. We highlight the prediction tools that can detect, segment, and track different mammalian cell morphologies across various image modalities and present a comparison of algorithms and unique features of these tools, whether they work locally or in the cloud. This would guide non-experts to determine which is best suited for their purposes and, developers to acknowledge what is worth further expansion. In addition, we provide a general discussion on potential implementations of the tools for a more extensive scope, which guides the reader to not restrict them to prediction tasks only. Finally, we conclude the article by stating new considerations for the development of interactive cell imaging tools and suggesting new directions for future research.
Collapse
Affiliation(s)
- Hafizi Malik
- Healthcare Engineering and Rehabilitation Research, Department of Mechatronics Engineering, International Islamic University Malaysia, Gombak, Selangor, Malaysia
| | - Ahmad Syahrin Idris
- Department of Electrical and Electronic Engineering, University of Southampton Malaysia, Iskandar Puteri, Johor, Malaysia
| | - Siti Fauziah Toha
- Healthcare Engineering and Rehabilitation Research, Department of Mechatronics Engineering, International Islamic University Malaysia, Gombak, Selangor, Malaysia
| | - Izyan Mohd Idris
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Muhammad Fauzi Daud
- Institute of Medical Science Technology, Universiti Kuala Lumpur, Kajang, Selangor, Malaysia
| | - Nur Liyana Azmi
- Healthcare Engineering and Rehabilitation Research, Department of Mechatronics Engineering, International Islamic University Malaysia, Gombak, Selangor, Malaysia
| |
Collapse
|
39
|
Zakharova A, Tashyreva D, Butenko A, Morales J, Saura A, Svobodová M, Poschmann G, Nandipati S, Zakharova A, Noyvert D, Gahura O, Týč J, Stühler K, Kostygov AY, Nowack ECM, Lukeš J, Yurchenko V. A neo-functionalized homolog of host transmembrane protein controls localization of bacterial endosymbionts in the trypanosomatid Novymonas esmeraldas. Curr Biol 2023:S0960-9822(23)00542-0. [PMID: 37201521 DOI: 10.1016/j.cub.2023.04.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 05/20/2023]
Abstract
The stability of endosymbiotic associations between eukaryotes and bacteria depends on a reliable mechanism ensuring vertical inheritance of the latter. Here, we demonstrate that a host-encoded protein, located at the interface between the endoplasmic reticulum of the trypanosomatid Novymonas esmeraldas and its endosymbiotic bacterium Ca. Pandoraea novymonadis, regulates such a process. This protein, named TMP18e, is a product of duplication and neo-functionalization of the ubiquitous transmembrane protein 18 (TMEM18). Its expression level is increased at the proliferative stage of the host life cycle correlating with the confinement of bacteria to the nuclear vicinity. This is important for the proper segregation of bacteria into the daughter host cells as evidenced from the TMP18e ablation, which disrupts the nucleus-endosymbiont association and leads to greater variability of bacterial cell numbers, including an elevated proportion of aposymbiotic cells. Thus, we conclude that TMP18e is necessary for the reliable vertical inheritance of endosymbionts.
Collapse
Affiliation(s)
- Alexandra Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Daria Tashyreva
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Jorge Morales
- Institute of Microbial Cell Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Michaela Svobodová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Gereon Poschmann
- Institute of Molecular Medicine, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Satish Nandipati
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Alena Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - David Noyvert
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Kai Stühler
- Institute of Microbial Cell Biology, Heinrich Heine University, 40225 Düsseldorf, Germany; Institute of Molecular Medicine, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Alexei Y Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| | - Eva C M Nowack
- Institute of Microbial Cell Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| |
Collapse
|
40
|
Laundon D, Katsamenis OL, Thompson J, Goggin P, Chatelet DS, Chavatte-Palmer P, Gostling NJ, Lewis RM. Correlative multiscale microCT-SBF-SEM imaging of resin-embedded tissue. Methods Cell Biol 2023; 177:241-267. [PMID: 37451769 DOI: 10.1016/bs.mcb.2023.01.014] [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] [Indexed: 07/18/2023]
Abstract
Three-dimensional biological microscopy presents a trade-off between spatial resolution and field of view. Correlative approaches applying multiple imaging techniques to the same sample can therefore mitigate against these trade-offs. Here, we present a workflow for correlative microscopic X-ray microfocus computed tomography (microCT) and serial block face scanning electron microscopy (SBF-SEM) imaging of resin-embedded tissue, using mammalian placental tissue samples as an example. This correlative X-ray and electron microscopy (CXEM) workflow allows users to image the same sample at multiple resolutions, and target the region of interest (ROI) for SBF-SEM based on microCT. We detail the protocols associated with this workflow and demonstrate its application in multiscale imaging of horse placental villi and ROI selection in the labyrinthine zone of a mouse placenta. These examples demonstrate how the protocol may need to be adapted for tissues with different densities.
Collapse
Affiliation(s)
- Davis Laundon
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Institute for Life Sciences, University of Southampton, Highfield, Southampton, United Kingdom
| | - Orestis L Katsamenis
- μ-VIS X-Ray Imaging Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, United Kingdom
| | - James Thompson
- Biomedical Imaging Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Patricia Goggin
- Biomedical Imaging Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - David S Chatelet
- Biomedical Imaging Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Pascale Chavatte-Palmer
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France; Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Neil J Gostling
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton, United Kingdom; Institute for Life Sciences, University of Southampton, Highfield, Southampton, United Kingdom
| | - Rohan M Lewis
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Institute for Life Sciences, University of Southampton, Highfield, Southampton, United Kingdom.
| |
Collapse
|
41
|
Palhol JSC, Balia M, Sánchez-Román Terán F, Labarchède M, Gontier E, Battefeld A. Direct association with the vascular basement membrane is a frequent feature of myelinating oligodendrocytes in the neocortex. Fluids Barriers CNS 2023; 20:24. [PMID: 37013659 PMCID: PMC10069068 DOI: 10.1186/s12987-023-00425-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Oligodendrocyte lineage cells interact with the vasculature in the gray matter. Physical and functional interactions between blood vessels and oligodendrocyte precursor cells play an essential role in both the developing and adult brain. Oligodendrocyte precursor cells have been shown to migrate along the vasculature and subsequently detach from it during their differentiation to oligodendrocytes. However, the association of mature oligodendrocytes with blood vessels has been noted since the discovery of this glial cell type almost a century ago, but this interaction remains poorly explored. RESULTS Here, we systematically investigated the extent of mature oligodendrocyte interaction with the vasculature in mouse brain. We found that ~ 17% of oligodendrocytes were in contact with blood vessels in the neocortex, the hippocampal CA1 region and the cerebellar cortex. Contacts were made mainly with capillaries and sparsely with larger arterioles or venules. By combining light and serial electron microscopy, we demonstrated that oligodendrocytes are in direct contact with the vascular basement membrane, raising the possibility of direct signaling pathways and metabolite exchange with endothelial cells. During experimental remyelination in the adult, oligodendrocytes were regenerated and associated with blood vessels in the same proportion compared to control cortex, suggesting a homeostatic regulation of the vasculature-associated oligodendrocyte population. CONCLUSIONS Based on their frequent and close association with blood vessels, we propose that vasculature-associated oligodendrocytes should be considered as an integral part of the brain vasculature microenvironment. This particular location could underlie specific functions of vasculature-associated oligodendrocytes, while contributing to the vulnerability of mature oligodendrocytes in neurological diseases.
Collapse
Affiliation(s)
- Justine S C Palhol
- Univ. Bordeaux, CNRS, IMN, UMR 5293, Bordeaux, F-33000, France
- Univ. Bordeaux, INSERM, Magendie, U1215, Bordeaux, F-33000, France
| | - Maddalena Balia
- Univ. Bordeaux, CNRS, IMN, UMR 5293, Bordeaux, F-33000, France
| | | | | | - Etienne Gontier
- Univ. Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UAR 3420, US 4, Bordeaux, F-33000, France
| | - Arne Battefeld
- Univ. Bordeaux, CNRS, IMN, UMR 5293, Bordeaux, F-33000, France.
| |
Collapse
|
42
|
Scharaw S, Sola-Carvajal A, Belevich I, Webb AT, Das S, Andersson S, Pentinmikko N, Villablanca EJ, Goldenring JR, Jokitalo E, Coffey RJ, Katajisto P. Golgi organization is a determinant of stem cell function in the small intestine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533814. [PMID: 36993731 PMCID: PMC10055334 DOI: 10.1101/2023.03.23.533814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cell-to-cell signalling between niche and stem cells regulates tissue regeneration. While the identity of many mediating factors is known, it is largely unknown whether stem cells optimize their receptiveness to niche signals according to the niche organization. Here, we show that Lgr5+ small intestinal stem cells (ISCs) regulate the morphology and orientation of their secretory apparatus to match the niche architecture, and to increase transport efficiency of niche signal receptors. Unlike the progenitor cells lacking lateral niche contacts, ISCs orient Golgi apparatus laterally towards Paneth cells of the epithelial niche, and divide Golgi into multiple stacks reflecting the number of Paneth cell contacts. Stem cells with a higher number of lateral Golgi transported Epidermal growth factor receptor (Egfr) with a higher efficiency than cells with one Golgi. The lateral Golgi orientation and enhanced Egfr transport required A-kinase anchor protein 9 (Akap9), and was necessary for normal regenerative capacity in vitro . Moreover, reduced Akap9 in aged ISCs renders ISCs insensitive to niche-dependent modulation of Golgi stack number and transport efficiency. Our results reveal stem cell-specific Golgi complex configuration that facilitates efficient niche signal reception and tissue regeneration, which is compromised in the aged epithelium.
Collapse
|
43
|
Jiao W, Chatton JY, Genoud C. Mitochondria morphometry in 3D datasets obtained from mouse brains with serial block-face scanning electron microscopy. Methods Cell Biol 2023; 177:197-211. [PMID: 37451767 DOI: 10.1016/bs.mcb.2023.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
The dysfunction of mitochondria is linked with many diseases. In the nervous system, evidence of their implication in neurodegenerative disease is growing. Mitochondria health is assessed by their impact on cellular metabolism but alterations in their morphologies and locations in the cells can also be markers of dysfunctions. Light microscopy techniques allow us to look at mitochondria in vivo in cells or tissue. But in the case of the nervous system, in order to assess the precise location of mitochondria in different cell types and neuronal compartments (cell bodies, dendrites or axons), electron microscopy is required. While the percentage of volume occupied by mitochondria can be assessed on 2D images, alterations in length, branching, and interactions with other organelles require three-dimensional (3D) segmentation of mitochondria in volumes imaged at ultrastructural level. Nowadays three-dimensional volume electron microscopy (vEM) imaging techniques such as serial block face scanning electron microscopy (SBF-SEM) enable us to image 3D volumes of tissue at ultrastructural level and can be done routinely. Segmentation of all the neuropil is also successfully achieved at a large scale in the nervous system. Here, we show a workflow based on open access resources, which allows us to image, segment, and analyze mitochondria in 3D volumes of regions of interest in the mouse brain. Taking advantage of recent developments, e.g., pre-trained models for mitochondria, we speed up the reconstruction and analysis. We also critically assess the impact on the results of the different reconstruction methods chosen and the level of manual corrections invested.
Collapse
Affiliation(s)
- Wei Jiao
- Electron Microscopy Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Jean-Yves Chatton
- Department of Fundamental Neurosciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Christel Genoud
- Electron Microscopy Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
44
|
Kalmbach L, Bourdon M, Belevich I, Safran J, Lemaire A, Heo JO, Otero S, Blob B, Pelloux J, Jokitalo E, Helariutta Y. Putative pectate lyase PLL12 and callose deposition through polar CALS7 are necessary for long-distance phloem transport in Arabidopsis. Curr Biol 2023; 33:926-939.e9. [PMID: 36805125 DOI: 10.1016/j.cub.2023.01.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 11/12/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
In plants, the phloem distributes photosynthetic products for metabolism and storage over long distances. It relies on specialized cells, the sieve elements, which are enucleated and interconnected through large so-called sieve pores in their adjoining cell walls. Reverse genetics identified PECTATE LYASE-LIKE 12 (PLL12) as critical for plant growth and development. Using genetic complementations, we established that PLL12 is required exclusively late during sieve element differentiation. Structural homology modeling, enzyme inactivation, and overexpression suggest a vital role for PLL12 in sieve-element-specific pectin remodeling. While short distance symplastic diffusion is unaffected, the pll12 mutant is unable to accommodate sustained plant development due to an incapacity to accommodate increasing hydraulic demands on phloem long-distance transport as the plant grows-a defect that is aggravated when combined with another sieve-element-specific mutant callose synthase 7 (cals7). Establishing CALS7 as a specific sieve pore marker, we investigated the subcellular dynamics of callose deposition in the developing sieve plate. Using fluorescent CALS7 then allowed identifying structural defects in pll12 sieve pores that are moderate at the cellular level but become physiologically relevant due to the serial arrangement of sieve elements in the sieve tube. Overall, pectin degradation through PLL12 appears subtle in quantitative terms. We therefore speculate that PLL12 may act as a regulator to locally remove homogalacturonan, thus potentially enabling further extracellular enzymes to access and modify the cell wall during sieve pore maturation.
Collapse
Affiliation(s)
- Lothar Kalmbach
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.
| | - Matthieu Bourdon
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Ilya Belevich
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Josip Safran
- UMR INRAE 1158 BioEcoAgro, BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Adrien Lemaire
- UMR INRAE 1158 BioEcoAgro, BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Jung-Ok Heo
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Sofia Otero
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Bernhard Blob
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Jérôme Pelloux
- UMR INRAE 1158 BioEcoAgro, BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Eija Jokitalo
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Ykä Helariutta
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
| |
Collapse
|
45
|
Biased IL-2 signals induce Foxp3-rich pulmonary lymphoid structures and facilitate long-term lung allograft acceptance in mice. Nat Commun 2023; 14:1383. [PMID: 36914624 PMCID: PMC10011523 DOI: 10.1038/s41467-023-36924-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Transplantation of solid organs can be life-saving in patients with end-stage organ failure, however, graft rejection remains a major challenge. In this study, by pre-conditioning with interleukin-2 (IL-2)/anti-IL-2 antibody complex treatment biased toward IL-2 receptor α, we achieved acceptance of fully mismatched orthotopic lung allografts that remained morphologically and functionally intact for more than 90 days in immunocompetent mice. These allografts are tolerated by the actions of forkhead box p3 (Foxp3)+ regulatory T (Treg) cells that home to the lung allografts. Although counts of circulating Treg cells rapidly return to baseline following cessation of IL-2 treatment, Foxp3+ Treg cells persist in peribronchial and peribronchiolar areas of the grafted lungs, forming organized clusters reminiscent of inducible tertiary lymphoid structures (iTLS). These iTLS in lung allografts are made of Foxp3+ Treg cells, conventional T cells, and B cells, as evidenced by using microscopy-based distribution and neighborhood analyses. Foxp3-transgenic mice with inducible and selective deletion of Foxp3+ cells are unable to form iTLS in lung allografts, and these mice acutely reject lung allografts. Collectively, we report that short-term, high-intensity and biased IL-2 pre-conditioning facilitates acceptance of vascularized and ventilated lung allografts without the need of immunosuppression, by inducing Foxp3-controlled iTLS formation within allografts.
Collapse
|
46
|
Chevrier DM, Juhin A, Menguy N, Bolzoni R, Soto-Rodriguez PED, Kojadinovic-Sirinelli M, Paterson GA, Belkhou R, Williams W, Skouri-Panet F, Kosta A, Le Guenno H, Pereiro E, Faivre D, Benzerara K, Monteil CL, Lefevre CT. Collective magnetotaxis of microbial holobionts is optimized by the three-dimensional organization and magnetic properties of ectosymbionts. Proc Natl Acad Sci U S A 2023; 120:e2216975120. [PMID: 36848579 PMCID: PMC10013862 DOI: 10.1073/pnas.2216975120] [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] [Received: 10/04/2022] [Accepted: 01/17/2023] [Indexed: 03/01/2023] Open
Abstract
Over the last few decades, symbiosis and the concept of holobiont-a host entity with a population of symbionts-have gained a central role in our understanding of life functioning and diversification. Regardless of the type of partner interactions, understanding how the biophysical properties of each individual symbiont and their assembly may generate collective behaviors at the holobiont scale remains a fundamental challenge. This is particularly intriguing in the case of the newly discovered magnetotactic holobionts (MHB) whose motility relies on a collective magnetotaxis (i.e., a magnetic field-assisted motility guided by a chemoaerotaxis system). This complex behavior raises many questions regarding how magnetic properties of symbionts determine holobiont magnetism and motility. Here, a suite of light-, electron- and X-ray-based microscopy techniques [including X-ray magnetic circular dichroism (XMCD)] reveals that symbionts optimize the motility, the ultrastructure, and the magnetic properties of MHBs from the microscale to the nanoscale. In the case of these magnetic symbionts, the magnetic moment transferred to the host cell is in excess (102 to 103 times stronger than free-living magnetotactic bacteria), well above the threshold for the host cell to gain a magnetotactic advantage. The surface organization of symbionts is explicitly presented herein, depicting bacterial membrane structures that ensure longitudinal alignment of cells. Magnetic dipole and nanocrystalline orientations of magnetosomes were also shown to be consistently oriented in the longitudinal direction, maximizing the magnetic moment of each symbiont. With an excessive magnetic moment given to the host cell, the benefit provided by magnetosome biomineralization beyond magnetotaxis can be questioned.
Collapse
Affiliation(s)
- Daniel M. Chevrier
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
| | - Amélie Juhin
- Sorbonne Université, UMR CNRS 7590, Muséum national d'Histoire naturelle (MNHN), Institut de recherche pour le développement (IRD), Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005Paris, France
| | - Nicolas Menguy
- Sorbonne Université, UMR CNRS 7590, Muséum national d'Histoire naturelle (MNHN), Institut de recherche pour le développement (IRD), Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005Paris, France
| | - Romain Bolzoni
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
| | - Paul E. D. Soto-Rodriguez
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
| | - Mila Kojadinovic-Sirinelli
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
| | - Greig A. Paterson
- Department of Earth, Ocean and Ecological Sciences, University of Liverpool, L69 7ZELiverpool, UK
| | - Rachid Belkhou
- Synchrotron Soleil, L'Orme des Merisiers, 91192Gif-sur-Yvette Cedex, France
| | - Wyn Williams
- School of GeoSciences, Grant Institute, University of Edinburgh, EdinburghEH9 3JW, UK
| | - Fériel Skouri-Panet
- Sorbonne Université, UMR CNRS 7590, Muséum national d'Histoire naturelle (MNHN), Institut de recherche pour le développement (IRD), Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005Paris, France
| | - Artemis Kosta
- Plateforme de Microscopie de l'Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, FR3479, Campus CNRS, 13402Marseille cedex 20, France
| | - Hugo Le Guenno
- Plateforme de Microscopie de l'Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, FR3479, Campus CNRS, 13402Marseille cedex 20, France
| | - Eva Pereiro
- ALBA Synchrotron Light Source, Cerdanyola del Vallés, Barcelona08290, Spain
| | - Damien Faivre
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
| | - Karim Benzerara
- Sorbonne Université, UMR CNRS 7590, Muséum national d'Histoire naturelle (MNHN), Institut de recherche pour le développement (IRD), Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005Paris, France
| | - Caroline L. Monteil
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
| | - Christopher T. Lefevre
- Aix-Marseille Université, Centre national de la recherche scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), UMR7265, Bioscience and biotechnology institute of Aix-Marseille (BIAM), Saint-Paul-lez-Durance13108, France
| |
Collapse
|
47
|
Senju Y, Mushtaq T, Vihinen H, Manninen A, Saarikangas J, Ven K, Engel U, Varjosalo M, Jokitalo E, Lappalainen P. Actin-rich lamellipodia-like protrusions contribute to the integrity of epithelial cell-cell junctions. J Biol Chem 2023; 299:104571. [PMID: 36871754 PMCID: PMC10173786 DOI: 10.1016/j.jbc.2023.104571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/11/2023] [Accepted: 02/01/2023] [Indexed: 03/06/2023] Open
Abstract
Metastasis-suppressor 1 (MTSS1) is a membrane-interacting scaffolding protein that regulates the integrity of epithelial cell-cell junctions and functions as a tumor suppressor in a wide range of carcinomas. MTSS1 binds phosphoinositide-rich membranes through its I-BAR domain, and is capable of sensing and generating negative membrane curvature in vitro. However, the mechanisms by which MTSS1 localizes to intercellular junctions in epithelial cells, and contributes to their integrity and maintenance have remained elusive. By carrying out electron microscopy and live-cell imaging on cultured Madin-Darby canine kidney (MDCK) cell monolayers, we provide evidence that adherens junctions of epithelial cells harbor lamellipodia-like, dynamic actin-driven membrane folds, which exhibit high negative membrane curvature at their distal edges. BioID proteomics and imaging experiments demonstrated that MTSS1 associates with an Arp2/3 complex activator, the WAVE-2 complex, in dynamic actin-rich protrusions at cell-cell junctions. Inhibition of Arp2/3 or WAVE-2 suppressed actin filament assembly at adherens junctions, decreased the dynamics of junctional membrane protrusions, and led to defects in epithelial integrity. Together, these results support a model in which membrane-associated MTSS1, together with the WAVE-2 and Arp2/3 complexes, promotes the formation of dynamic lamellipodia-like actin protrusions that contribute to the integrity of cell-cell junctions in epithelial monolayers.
Collapse
Affiliation(s)
- Yosuke Senju
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Japan.
| | - Toiba Mushtaq
- Helsinki Institute of Life Science (HiLIFE) - Institute of Biotechnology, University of Helsinki, Finland
| | - Helena Vihinen
- Helsinki Institute of Life Science (HiLIFE) - Institute of Biotechnology, University of Helsinki, Finland
| | - Aki Manninen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Finland
| | - Juha Saarikangas
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Finland; Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, Neuroscience Center, University of Helsinki, Finland
| | - Katharina Ven
- Helsinki Institute of Life Science (HiLIFE) - Institute of Biotechnology, University of Helsinki, Finland
| | - Ulrike Engel
- Nikon Imaging Center and Centre for Organismal Studies, Heidelberg University, Germany
| | - Markku Varjosalo
- Helsinki Institute of Life Science (HiLIFE) - Institute of Biotechnology, University of Helsinki, Finland
| | - Eija Jokitalo
- Helsinki Institute of Life Science (HiLIFE) - Institute of Biotechnology, University of Helsinki, Finland
| | - Pekka Lappalainen
- Helsinki Institute of Life Science (HiLIFE) - Institute of Biotechnology, University of Helsinki, Finland
| |
Collapse
|
48
|
Steyer AM, Buscham TJ, Lorenz C, Hümmert S, Eichel-Vogel MA, Schadt LC, Edgar JM, Köster S, Möbius W, Nave KA, Werner HB. Focused ion beam-scanning electron microscopy links pathological myelin outfoldings to axonal changes in mice lacking Plp1 or Mag. Glia 2023; 71:509-523. [PMID: 36354016 DOI: 10.1002/glia.24290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022]
Abstract
Healthy myelin sheaths consist of multiple compacted membrane layers closely encasing the underlying axon. The ultrastructure of CNS myelin requires specialized structural myelin proteins, including the transmembrane-tetraspan proteolipid protein (PLP) and the Ig-CAM myelin-associated glycoprotein (MAG). To better understand their functional relevance, we asked to what extent the axon/myelin-units display similar morphological changes if PLP or MAG are lacking. We thus used focused ion beam-scanning electron microscopy (FIB-SEM) to re-investigate axon/myelin-units side-by-side in Plp- and Mag-null mutant mice. By three-dimensional reconstruction and morphometric analyses, pathological myelin outfoldings extend up to 10 μm longitudinally along myelinated axons in both models. More than half of all assessed outfoldings emerge from internodal myelin. Unexpectedly, three-dimensional reconstructions demonstrated that both models displayed complex axonal pathology underneath the myelin outfoldings, including axonal sprouting. Axonal anastomosing was additionally observed in Plp-null mutant mice. Importantly, normal-appearing axon/myelin-units displayed significantly increased axonal diameters in both models according to quantitative assessment of electron micrographs. These results imply that healthy CNS myelin sheaths facilitate normal axonal diameters and shape, a function that is impaired when structural myelin proteins PLP or MAG are lacking.
Collapse
Affiliation(s)
- Anna M Steyer
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Electron Microscopy-City Campus, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Tobias J Buscham
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Charlotta Lorenz
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Sophie Hümmert
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Maria A Eichel-Vogel
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Leonie C Schadt
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Julia M Edgar
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany.,Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Wiebke Möbius
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Electron Microscopy-City Campus, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Klaus-Armin Nave
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Hauke B Werner
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| |
Collapse
|
49
|
Świątek P, Novo M, Marchán DF, Gajda Ł, Małota K, Urbisz AZ. Ovary micromorphology in hormogastrid earthworms with a particular emphasis on the organization of the germline cysts. ZOOLOGY 2023; 158:126081. [PMID: 36871333 DOI: 10.1016/j.zool.2023.126081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/22/2022] [Accepted: 02/24/2023] [Indexed: 03/02/2023]
Abstract
There is a gap in our knowledge of microorganization and the functioning of ovaries in earthworms (Crassiclitellata) and allied taxa. Recent analyses of ovaries in microdriles and leech-like taxa revealed that they are composed of syncytial germline cysts accompanied by somatic cells. Although the pattern of cyst organization is conserved across Clitellata - each cell is connected via one intercellular bridge (ring canal) to the central and anuclear cytoplasmic mass termed the cytophore - this system shows high evolutionary plasticity. In Crassiclitellata, only the gross morphology of ovaries and their segmental localization is well known, whereas ultrastructural data are limited to lumbricids like Dendrobaena veneta. Here we present the first report about ovarian histology and ultrastructure in Hormogastridae, a small family of earthworms inhabiting the western parts of the Mediterranean sea basin. We analyzed three species from three different genera and showed that the pattern of ovary organization is the same within this taxon. Ovaries are cone-like, with a broad part connected to the septum and a narrow distal end forming an egg string. Ovaries are composed of numerous cysts uniting a small number of cells, eight in Carpetania matritensis. There is a gradient of cysts development along the long ovary axis, and three zones can be distinguished. In zone I, cysts develop in complete synchrony and unite oogonia and early meiotic cells (till diplotene). Then (zone II), the synchrony is lost, and one cell (prospective oocyte) grows faster than the rest (prospective nurse cells). In zone III, oocytes pass the growth phase and gather nutrients; at this time, their contact with the cytophore is lost. Nurse cells grow slightly, eventually die via apoptosis, and are removed by coelomocytes. The most characteristic feature of hormogastrid germ cysts is the inconspicuous cytophore in the form of thread-like thin cytoplasmic strands (reticular cytophore). We found that the ovary organization in studied hormogastrids is very similar to that described for D. veneta and propose the term "Dendrobaena" type of ovaries. We expect the same microorganization of ovaries will be found in other hormogastrids and lumbricids.
Collapse
Affiliation(s)
- Piotr Świątek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007 Katowice, Poland.
| | - Marta Novo
- Departmento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Nováis, 12, 28040 Madrid, Spain
| | - Daniel Fernández Marchán
- Departmento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Nováis, 12, 28040 Madrid, Spain; UMR, CEFE, CNRS, 1919 route de Mende, 34293 Montpellier Cedex 5, France
| | - Łukasz Gajda
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007 Katowice, Poland
| | - Karol Małota
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007 Katowice, Poland
| | - Anna Z Urbisz
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007 Katowice, Poland
| |
Collapse
|
50
|
Massive Accumulation of Strontium and Barium in Diplonemid Protists. mBio 2023; 14:e0327922. [PMID: 36645306 PMCID: PMC9972996 DOI: 10.1128/mbio.03279-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Barium and strontium are often used as proxies of marine productivity in palaeoceanographic reconstructions of global climate. However, long-searched biological drivers for such correlations remain unknown. Here, we report that taxa within one of the most abundant groups of marine planktonic protists, diplonemids (Euglenozoa), are potent accumulators of intracellular barite (BaSO4), celestite (SrSO4), and strontiobarite (Ba,Sr)SO4. In culture, Namystinia karyoxenos accumulates Ba2+ and Sr2+ 42,000 and 10,000 times higher than the surrounding medium, forming barite and celestite representing 90% of the dry weight, the greatest concentration in biomass known to date. As heterotrophs, diplonemids are not restricted to the photic zone, and they are widespread in the oceans in astonishing abundance and diversity, as their distribution correlates with environmental particulate barite and celestite, prevailing in the mesopelagic zone. We found diplonemid predators, the filter-feeding zooplankton that produces fecal pellets containing the undigested celestite from diplonemids, facilitating its deposition on the seafloor. To the best of our knowledge, evidence for diplonemid biomineralization presents the strongest explanation for the occurrence of particulate barite and celestite in the marine environment. Both structures of the crystals and their variable chemical compositions found in diplonemids fit the properties of environmentally sampled particulate barite and celestite. Finally, we propose that diplonemids, which emerged during the Neoproterozoic era, qualify as impactful players in Ba2+/Sr2+ cycling in the ocean that has possibly contributed to sedimentary rock formation over long geological periods. IMPORTANCE We have identified that diplonemids, an abundant group of marine planktonic protists, accumulate conspicuous amounts of Sr2+ and Ba2+ in the form of intracellular barite and celestite crystals, in concentrations that greatly exceed those of the most efficient Ba/Sr-accumulating organisms known to date. We propose that diplonemids are potential players in Ba2+/Sr2+ cycling in the ocean and have possibly contributed to sedimentary rock formation over long geological periods. These organisms emerged during the Neoproterozoic era (590 to 900 million years ago), prior to known coccolithophore carbonate biomineralization (~200 million years ago). Based on reported data, the distribution of diplonemids in the oceans is correlated with the occurrence of particulate barite and celestite. Finally, diplonemids may provide new insights into the long-questioned biogenic origin of particulate barite and celestite and bring more understanding of the observed spatial-temporal correlation of the minerals with marine productivity used in reconstructions of past global climate.
Collapse
|