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Lee V, Hinton BT, Hirashima T. Collective cell dynamics and luminal fluid flow in the epididymis: A mechanobiological perspective. Andrology 2024; 12:939-948. [PMID: 37415418 PMCID: PMC11278975 DOI: 10.1111/andr.13490] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/08/2023] [Accepted: 07/04/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND The mammalian epididymis is a specialized duct system that serves a critical role in sperm maturation and storage. Its distinctive, highly coiled tissue morphology provides a unique opportunity to investigate the link between form and function in reproductive biology. Although recent genetic studies have identified key genes and signaling pathways involved in the development and physiological functions of the epididymis, there has been limited discussion about the underlying dynamic and mechanical processes that govern these phenomena. AIMS In this review, we aim to address this gap by examining two key aspects of the epididymis across its developmental and physiological phases. RESULTS AND DISCUSSION First, we discuss how the complex morphology of the Wolffian/epididymal duct emerges through collective cell dynamics, including duct elongation, cell proliferation, and arrangement during embryonic development. Second, we highlight dynamic aspects of luminal fluid flow in the epididymis, essential for regulating the microenvironment for sperm maturation and motility, and discuss how this phenomenon emerges and interplays with epididymal epithelial cells. CONCLUSION This review not only aims to summarize current knowledge but also to provide a starting point for further exploration of mechanobiological aspects related to the cellular and extracellular fluid dynamics in the epididymis.
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Affiliation(s)
- Veronica Lee
- Mechanobiology, Institute, National University of Singapore, Singapore, Singapore
| | - Barry T. Hinton
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Tsuyoshi Hirashima
- Mechanobiology, Institute, National University of Singapore, Singapore, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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2
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Echeverria CV, Leathers TA, Rogers CD. Effectiveness of fixation methods for wholemount immunohistochemistry across cellular compartments in chick embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.23.586361. [PMID: 38585750 PMCID: PMC10996528 DOI: 10.1101/2024.03.23.586361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The choice of fixation method significantly impacts tissue morphology and protein visualization after immunohistochemistry (IHC). In this study, we compared the effects of paraformaldehyde (PFA) and trichloroacetic acid (TCA) fixation prior to IHC on chicken embryos. Our findings underscore the importance of validating fixation methods for accurate interpretation of IHC results, with implications for antibody validation and tissue-specific protein localization studies. We found that TCA fixation resulted in larger and more circular nuclei compared to PFA fixation. Additionally, TCA fixation altered the appearance of subcellular localization and fluorescence intensity of various proteins, including transcription factors and cytoskeletal proteins. Notably, TCA fixation revealed protein localization domains that may be inaccessible with PFA fixation. These results highlight the need for optimization of fixation protocols depending on the target epitope and model system, emphasizing the importance of methodological considerations in biological analyses.
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Affiliation(s)
- Camilo V Echeverria
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, Davis, CA, USA
| | - Tess A Leathers
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, Davis, CA, USA
| | - Crystal D Rogers
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, Davis, CA, USA
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3
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Hirashima T, Matsuda M. ERK-mediated curvature feedback regulates branching morphogenesis in lung epithelial tissue. Curr Biol 2024; 34:683-696.e6. [PMID: 38228149 DOI: 10.1016/j.cub.2023.12.049] [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: 07/14/2022] [Revised: 11/06/2023] [Accepted: 12/14/2023] [Indexed: 01/18/2024]
Abstract
Intricate branching patterns emerge in internal organs due to the recurrent occurrence of simple deformations in epithelial tissues. During murine lung development, epithelial cells in distal tips of the single tube require fibroblast growth factor (FGF) signals emanating from their surrounding mesenchyme to form repetitive tip bifurcations. However, it remains unknown how the cells employ FGF signaling to convert their behaviors to achieve the recursive branching processes. Here, we show a mechano-chemical regulatory system underlying lung branching morphogenesis, orchestrated by extracellular signal-regulated kinase (ERK) as a downstream driver of FGF signaling. We found that tissue-scale curvature regulated ERK activity in the lung epithelium using two-photon live cell imaging and mechanical perturbations. ERK activation occurs specifically in epithelial tissues exhibiting positive curvature, regardless of whether the change in curvature was attributable to morphogenesis or perturbations. Moreover, ERK activation accelerates actin polymerization preferentially at the apical side of cells, mechanically contributing to the extension of the apical membrane, culminating in a reduction of epithelial tissue curvature. These results indicate the existence of a negative feedback loop between tissue curvature and ERK activity that transcends spatial scales. Our mathematical model confirms that this regulatory mechanism is sufficient to generate the recursive branching processes. Taken together, we propose that ERK orchestrates a curvature feedback loop pivotal to the self-organized patterning of tissues.
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Affiliation(s)
- Tsuyoshi Hirashima
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive MD9, Singapore 117593, Singapore; The Hakubi Center, Kyoto University, Yoshida-honmachi, Kyoto 606-8501, Japan; Graduate School of Biostudies, Kyoto University, Yoshidakone-cho, Kyoto 606-8501, Japan; Japan Science and Technology Agency, PRESTO, 4-1-8 Honchō, Kawaguchi 332-0012, Japan.
| | - Michiyuki Matsuda
- Graduate School of Biostudies, Kyoto University, Yoshidakone-cho, Kyoto 606-8501, Japan; Graduate School of Medicine, Kyoto University, Yoshidakone-cho, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-honmachi, Kyoto 606-8317, Japan
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4
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Ishii M, Tateya T, Matsuda M, Hirashima T. Stalling interkinetic nuclear migration in curved pseudostratified epithelium of developing cochlea. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211024. [PMID: 34909216 PMCID: PMC8652271 DOI: 10.1098/rsos.211024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/05/2021] [Indexed: 05/15/2023]
Abstract
The bending of epithelial tubes is a fundamental process in organ morphogenesis, driven by various multicellular behaviours. The cochlea in the mammalian inner ear is a representative example of spiral tissue architecture where the continuous bending of the duct is a fundamental component of its morphogenetic process. Although the cochlear duct morphogenesis has been studied by genetic approaches extensively, it is still unclear how the cochlear duct morphology is physically formed. Here, we report that nuclear behaviour changes are associated with the curvature of the pseudostratified epithelium during murine cochlear development. Two-photon live-cell imaging reveals that the nuclei shuttle between the luminal and basal edges of the cell is in phase with cell-cycle progression, known as interkinetic nuclear migration, in the flat region of the pseudostratified epithelium. However, the nuclei become stationary on the luminal side following mitosis in the curved region. Mathematical modelling together with perturbation experiments shows that this nuclear stalling facilitates luminal-basal differential growth within the epithelium, suggesting that the nuclear stalling would contribute to the bending of the pseudostratified epithelium during the cochlear duct development. The findings suggest a possible scenario of differential growth which sculpts the tissue shape, driven by collective nuclear dynamics.
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Affiliation(s)
- Mamoru Ishii
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Tomoko Tateya
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Speech and Hearing Sciences and Disorders, Faculty of Health and Medical Sciences, Kyoto University of Advanced Science, Kyoto, Japan
| | - Michiyuki Matsuda
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
| | - Tsuyoshi Hirashima
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- The Hakubi Center, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Japan Science and Technology Agency, PRESTO, Kawaguchi, Japan
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5
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Kumegawa S, Yamada G, Hashimoto D, Hirashima T, Kajimoto M, Isono K, Fujimoto K, Suzuki K, Uemura K, Ema M, Asamura S. Development of Surgical and Visualization Procedures to Analyze Vasculatures by Mouse Tail Edema Model. Biol Proced Online 2021; 23:21. [PMID: 34758723 PMCID: PMC8582144 DOI: 10.1186/s12575-021-00159-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/26/2021] [Indexed: 12/02/2022] Open
Abstract
Background Because of the high frequency of chronic edema formation in the current “aged” society, analyses and detailed observation of post-surgical edema are getting more required. Post-surgical examination of the dynamic vasculature including L.V. (Lymphatic Vasculature) to monitor edema formation has not been efficiently performed. Hence, procedures for investigating such vasculature are essential. By inserting transparent sheet into the cutaneous layer of mouse tails as a novel surgery model (theTailEdema bySilicone sheet mediatedTransparency protocol; TEST), the novel procedures are introduced and analyzed by series of histological analyses including video-based L.V. observation and 3D histological reconstruction of vasculatures in mouse tails. Results The dynamic generation of post-surgical main and fine (neo) L.V. connective structure during the edematous recovery process was visualized by series of studies with a novel surgery model. Snapshot images taken from live binocular image recording for TEST samples suggested the presence of main and elongating fine (neo) L.V. structure. After the ligation of L.V., the enlargement of main L.V. was confirmed. In the case of light sheet fluorescence microscopy (LSFM) observation, such L.V. connections were also suggested by using transparent 3D samples. Finally, the generation of neo blood vessels particularly in the region adjacent to the silicone sheet and the operated boundary region was suggested in 3D reconstruction images. However, direct detection of elongating fine (neo) L.V. was not suitable for analysis by such LSFM and 3D reconstruction procedures. Thus, such methods utilizing fixed tissues are appropriate for general observation for the operated region including of L.V. Conclusions The current surgical procedures and analysis on the post-surgical status are the first case to observe vasculatures in vivo with a transparent sheet. Systematic analyses including the FITC-dextran mediated snap shot images observation suggest the elongation of fine (neo) lymphatic vasculature. Post-surgical analyses including LSFM and 3D histological structural reconstruction, are suitable to reveal the fixed structures of blood and lymphatic vessels formation. Supplementary Information The online version contains supplementary material available at 10.1186/s12575-021-00159-3.
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Affiliation(s)
- Shinji Kumegawa
- Department of Plastic and Reconstructive Surgery, Graduate School of Medicine, Medical University of Wakayama, Wakayama, Japan
| | - Gen Yamada
- Department of Developmental Genetics, Institute of Advanced Medicine, Medical University of Wakayama, Wakayama, Japan.
| | - Daiki Hashimoto
- Department of molecular Physiology, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Tsuyoshi Hirashima
- The Hakubi Center/Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Mizuki Kajimoto
- Department of Developmental Genetics, Institute of Advanced Medicine, Medical University of Wakayama, Wakayama, Japan
| | - Kyoichi Isono
- Laboratory Animal Center, Wakayama Medical University, Wakayama, Japan
| | - Kota Fujimoto
- Department of Developmental Genetics, Institute of Advanced Medicine, Medical University of Wakayama, Wakayama, Japan
| | - Kentaro Suzuki
- Department of Developmental Genetics, Institute of Advanced Medicine, Medical University of Wakayama, Wakayama, Japan
| | - Kazuhisa Uemura
- Department of Plastic and Reconstructive Surgery, Graduate School of Medicine, Medical University of Wakayama, Wakayama, Japan
| | - Masatsugu Ema
- Department of Stem Cells and Human Diseases Models, Research Center for Animal Life Science, Medical University of Shiga, Otsu, Shiga, Japan
| | - Shinichi Asamura
- Department of Plastic and Reconstructive Surgery, Graduate School of Medicine, Medical University of Wakayama, Wakayama, Japan
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6
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Ishii M, Tateya T, Matsuda M, Hirashima T. Retrograde ERK activation waves drive base-to-apex multicellular flow in murine cochlear duct morphogenesis. eLife 2021; 10:e61092. [PMID: 33667159 PMCID: PMC7935486 DOI: 10.7554/elife.61092] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/23/2021] [Indexed: 12/17/2022] Open
Abstract
A notable example of spiral architecture in organs is the mammalian cochlear duct, where the morphology is critical for hearing function. Genetic studies have revealed necessary signaling molecules, but it remains unclear how cellular dynamics generate elongating, bending, and coiling of the cochlear duct. Here, we show that extracellular signal-regulated kinase (ERK) activation waves control collective cell migration during the murine cochlear duct development using deep tissue live-cell imaging, Förster resonance energy transfer (FRET)-based quantitation, and mathematical modeling. Long-term FRET imaging reveals that helical ERK activation propagates from the apex duct tip concomitant with the reverse multicellular flow on the lateral side of the developing cochlear duct, resulting in advection-based duct elongation. Moreover, model simulations, together with experiments, explain that the oscillatory wave trains of ERK activity and the cell flow are generated by mechanochemical feedback. Our findings propose a regulatory mechanism to coordinate the multicellular behaviors underlying the duct elongation during development.
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Affiliation(s)
- Mamoru Ishii
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
| | - Tomoko Tateya
- Department of Speech and Hearing Sciences and Disorders, Faculty of Health and Medical Sciences, Kyoto University of Advanced ScienceKyotoJapan
| | - Michiyuki Matsuda
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
- Graduate School of Medicine, Kyoto UniversityKyotoJapan
| | - Tsuyoshi Hirashima
- Graduate School of Biostudies, Kyoto UniversityKyotoJapan
- The Hakubi Center, Kyoto UniversityKyotoJapan
- Japan Science and Technology Agency, PRESTOKawaguchiJapan
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7
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Yoshida T, Matsuda M, Hirashima T. Incoherent Feedforward Regulation via Sox9 and ERK Underpins Mouse Tracheal Cartilage Development. Front Cell Dev Biol 2020; 8:585640. [PMID: 33195234 PMCID: PMC7642454 DOI: 10.3389/fcell.2020.585640] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/15/2020] [Indexed: 11/13/2022] Open
Abstract
Tracheal cartilage provides architectural integrity to the respiratory airway, and defects in this structure during embryonic development cause severe congenital anomalies. Previous genetic studies have revealed genes that are critical for the development of tracheal cartilage. However, it is still unclear how crosstalk between these proteins regulates tracheal cartilage formation. Here we show a core regulatory network underlying murine tracheal chondrogenesis from embryonic day (E) 12.5 to E15.5, by combining volumetric imaging of fluorescence reporters, inhibitor assays, and mathematical modeling. We focused on SRY-box transcription factor 9 (Sox9) and extracellular signal-regulated kinase (ERK) in the tracheal mesenchyme, and observed a synchronous, inverted U-shaped temporal change in both Sox9 expression and ERK activity with a peak at E14.5, whereas the expression level of downstream cartilage matrix genes, such as collagen II alpha 1 (Col2a1) and aggrecan (Agc1), monotonically increased. Inhibitor assays revealed that the ERK signaling pathway functions as an inhibitory regulator of tracheal cartilage differentiation during this period. These results suggest that expression of the cartilage matrix genes is controlled by an incoherent feedforward loop via Sox9 and ERK, which is supported by a mathematical model. Furthermore, the modeling analysis suggests that a Sox9-ERK incoherent feedforward regulation augments the robustness against the variation of upstream factors. The present study provides a better understanding of the regulatory network underlying the tracheal development and will be helpful for efficient induction of tracheal organoids.
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Affiliation(s)
- Takuya Yoshida
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Michiyuki Matsuda
- Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tsuyoshi Hirashima
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Japan Science and Technology Agency, PRESTO, Tokyo, Japan
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8
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Gómez-Gaviro MV, Sanderson D, Ripoll J, Desco M. Biomedical Applications of Tissue Clearing and Three-Dimensional Imaging in Health and Disease. iScience 2020; 23:101432. [PMID: 32805648 PMCID: PMC7452225 DOI: 10.1016/j.isci.2020.101432] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/27/2022] Open
Abstract
Three-dimensional (3D) optical imaging techniques can expand our knowledge about physiological and pathological processes that cannot be fully understood with 2D approaches. Standard diagnostic tests frequently are not sufficient to unequivocally determine the presence of a pathological condition. Whole-organ optical imaging requires tissue transparency, which can be achieved by using tissue clearing procedures enabling deeper image acquisition and therefore making possible the analysis of large-scale biological tissue samples. Here, we review currently available clearing agents, methods, and their application in imaging of physiological or pathological conditions in different animal and human organs. We also compare different optical tissue clearing methods discussing their advantages and disadvantages and review the use of different 3D imaging techniques for the visualization and image acquisition of cleared tissues. The use of optical tissue clearing resources for large-scale biological tissues 3D imaging paves the way for future applications in translational and clinical research.
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Affiliation(s)
- Maria Victoria Gómez-Gaviro
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain.
| | - Daniel Sanderson
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain
| | - Jorge Ripoll
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain
| | - Manuel Desco
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain; Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
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9
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Hirashima T. Mechanical Tissue Compression and Whole-mount Imaging at Single CellResolution for Developing Murine Epididymal Tubules. Bio Protoc 2020; 10:e3694. [PMID: 33659362 DOI: 10.21769/bioprotoc.3694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 11/02/2022] Open
Abstract
Cells inside the body are subjected to various mechanical stress, such as stretch or compression provided by surrounding cells, shear stresses by blood or lymph flows, and normal stresses by luminal liquids. Force loading to the biological tissues is a fundamental method to better understand cellular responses to such mechanical stimuli. There have been many studies on compression or stretch experiments that target culture cells attached to a flexible extensible material including polydimethylsiloxane (PDMS); however, the know-how of those targeting to tissues is still incomplete. Here we present the protocol for mechanical tissue compression and image-based analysis by focusing on developing murine epididymis as an example. We show a series of steps including tissue dissection from murine embryos, hydrogel-based compression method using a manual device, and non-destructive volumetric tissue imaging. This protocol is useful for quantifying and exploring the biological mechanoresponse system at tissue level.
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Affiliation(s)
- Tsuyoshi Hirashima
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Japan Science and Technology Agency, PRESTO, Sakyo-ku, Kyoto, Japan
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10
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Hirashima T, Adachi T. Polarized cellular mechano-response system for maintaining radial size in developing epithelial tubes. Development 2019; 146:dev.181206. [PMID: 31619390 PMCID: PMC6918744 DOI: 10.1242/dev.181206] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/07/2019] [Indexed: 12/31/2022]
Abstract
Size control in biological tissues involves multicellular communication via mechanical forces during development. Although fundamental cellular behaviours in response to mechanical stimuli underlie size maintenance during morphogenetic processes, the mechanisms underpinning the cellular mechano-response system that maintains size along an axis of a polarized tissue remain elusive. Here, we show how the diameter of an epithelial tube is maintained during murine epididymal development by combining quantitative imaging, mechanical perturbation and mathematical modelling. We found that epithelial cells counteract compressive forces caused by cell division exclusively along the circumferential axis of the tube to produce polarized contractile forces, eventually leading to an oriented cell rearrangement. Moreover, a mathematical model that includes the polarized mechano-responsive regime explains how the diameter of proliferating tubes is maintained. Our findings pave the way for an improved understanding of the cellular response to mechanical forces that involves collective multicellular behaviours for organizing diverse tissue morphologies. Summary: Polarized cellular constriction responding to mechanical stress controls the diameter of a developing epithelial tube during murine epididymal development.
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Affiliation(s)
- Tsuyoshi Hirashima
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, 6068501, Kyoto, Japan .,Institute for Frontier Life and Medical Sciences, Kyoto University, 6068501, Kyoto, Japan
| | - Taiji Adachi
- Institute for Frontier Life and Medical Sciences, Kyoto University, 6068501, Kyoto, Japan
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11
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Gradinaru V, Treweek J, Overton K, Deisseroth K. Hydrogel-Tissue Chemistry: Principles and Applications. Annu Rev Biophys 2019; 47:355-376. [PMID: 29792820 PMCID: PMC6359929 DOI: 10.1146/annurev-biophys-070317-032905] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the past five years, a rapidly developing experimental approach has enabled high-resolution and high-content information retrieval from intact multicellular animal (metazoan) systems. New chemical and physical forms are created in the hydrogel-tissue chemistry process, and the retention and retrieval of crucial phenotypic information regarding constituent cells and molecules (and their joint interrelationships) are thereby enabled. For example, rich data sets defining both single-cell-resolution gene expression and single-cell-resolution activity during behavior can now be collected while still preserving information on three-dimensional positioning and/or brain-wide wiring of those very same neurons-even within vertebrate brains. This new approach and its variants, as applied to neuroscience, are beginning to illuminate the fundamental cellular and chemical representations of sensation, cognition, and action. More generally, reimagining metazoans as metareactants-or positionally defined three-dimensional graphs of constituent chemicals made available for ongoing functionalization, transformation, and readout-is stimulating innovation across biology and medicine.
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Affiliation(s)
- Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Jennifer Treweek
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Kristin Overton
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA;
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA; .,Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305, USA.,H oward Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
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12
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Berg EM, Björnfors ER, Pallucchi I, Picton LD, El Manira A. Principles Governing Locomotion in Vertebrates: Lessons From Zebrafish. Front Neural Circuits 2018; 12:73. [PMID: 30271327 PMCID: PMC6146226 DOI: 10.3389/fncir.2018.00073] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/27/2018] [Indexed: 11/24/2022] Open
Abstract
Locomotor behaviors are critical for survival and enable animals to navigate their environment, find food and evade predators. The circuits in the brain and spinal cord that initiate and maintain such different modes of locomotion in vertebrates have been studied in numerous species for over a century. In recent decades, the zebrafish has emerged as one of the main model systems for the study of locomotion, owing to its experimental amenability, and work in zebrafish has revealed numerous new insights into locomotor circuit function. Here, we review the literature that has led to our current understanding of the neural circuits controlling swimming and escape in zebrafish. We highlight recent studies that have enriched our comprehension of key topics, such as the interactions between premotor excitatory interneurons (INs) and motoneurons (MNs), supraspinal and spinal circuits that coordinate escape maneuvers, and developmental changes in overall circuit composition. We also discuss roles for neuromodulators and sensory inputs in modifying the relative strengths of constituent circuit components to provide flexibility in zebrafish behavior, allowing the animal to accommodate changes in the environment. We aim to provide a coherent framework for understanding the circuitry in the brain and spinal cord of zebrafish that allows the animal to flexibly transition between different speeds, and modes, of locomotion.
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Affiliation(s)
- Eva M Berg
- Department of Neuroscience, Karolinska Institute (KI), Stockholm, Sweden
| | | | - Irene Pallucchi
- Department of Neuroscience, Karolinska Institute (KI), Stockholm, Sweden
| | - Laurence D Picton
- Department of Neuroscience, Karolinska Institute (KI), Stockholm, Sweden
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13
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Hirashima T, Hoshuyama M, Adachi T. In vitro tubulogenesis of Madin–Darby canine kidney (MDCK) spheroids occurs depending on constituent cell number and scaffold gel concentration. J Theor Biol 2017; 435:110-115. [DOI: 10.1016/j.jtbi.2017.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 08/23/2017] [Accepted: 09/11/2017] [Indexed: 02/06/2023]
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14
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Jensen KHR, Berg RW. Advances and perspectives in tissue clearing using CLARITY. J Chem Neuroanat 2017; 86:19-34. [DOI: 10.1016/j.jchemneu.2017.07.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/12/2017] [Accepted: 07/12/2017] [Indexed: 12/16/2022]
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15
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Nojima S, Susaki EA, Yoshida K, Takemoto H, Tsujimura N, Iijima S, Takachi K, Nakahara Y, Tahara S, Ohshima K, Kurashige M, Hori Y, Wada N, Ikeda JI, Kumanogoh A, Morii E, Ueda HR. CUBIC pathology: three-dimensional imaging for pathological diagnosis. Sci Rep 2017; 7:9269. [PMID: 28839164 PMCID: PMC5571108 DOI: 10.1038/s41598-017-09117-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/21/2017] [Indexed: 12/11/2022] Open
Abstract
The examination of hematoxylin and eosin (H&E)-stained tissues on glass slides by conventional light microscopy is the foundation for histopathological diagnosis. However, this conventional method has some limitations in x-y axes due to its relatively narrow range of observation area and in z-axis due to its two-dimensionality. In this study, we applied a CUBIC pipeline, which is the most powerful tissue-clearing and three-dimensional (3D)-imaging technique, to clinical pathology. CUBIC was applicable to 3D imaging of both normal and abnormal patient-derived, human lung and lymph node tissues. Notably, the combination of deparaffinization and CUBIC enabled 3D imaging of specimens derived from paraffin-embedded tissue blocks, allowing quantitative evaluation of nuclear and structural atypia of an archival malignant lymphoma tissue. Furthermore, to examine whether CUBIC can be applied to practical use in pathological diagnosis, we performed a histopathological screening of a lymph node metastasis based on CUBIC, which successfully improved the sensitivity in detecting minor metastatic carcinoma nodules in lymph nodes. Collectively, our results indicate that CUBIC significantly contributes to retrospective and prospective clinicopathological diagnosis, which might lead to the establishment of a novel field of medical science based on 3D histopathology.
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Affiliation(s)
- Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Immunopathology, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Etsuo A Susaki
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Kyotaro Yoshida
- Department of Pathology, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Hiroyoshi Takemoto
- Department of Surgery, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Naoto Tsujimura
- Department of Surgery, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Shohei Iijima
- Department of Nutrition Oncology, Osaka International Cancer Institute, 3-1-69, Otemae, Chuo-ku, Osaka-shi, Osaka, 541-8567, Japan
| | - Ko Takachi
- Department of Surgery, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Yujiro Nakahara
- Department of Surgery, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Shinichiro Tahara
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kenji Ohshima
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masako Kurashige
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yumiko Hori
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Naoki Wada
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jun-Ichiro Ikeda
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Atsushi Kumanogoh
- Department of Immunopathology, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Respiratory Medicine, Allergy and Rheumatic Disease, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Eiichi Morii
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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16
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Kumar M, Tanwar P. Organ Culture and Whole Mount Immunofluorescence Staining of Mouse Wolffian Ducts. J Vis Exp 2017. [PMID: 28117794 DOI: 10.3791/55134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Tubal morphogenesis is a fundamental requirement for the development of most mammalian organs, including the male reproductive system. The epididymis, an integral part of the male reproductive tract, is responsible for sperm storage, maturation, and transport. The adult epididymis is a highly coiled tube that develops from a simple and straight embryonic precursor known as Wolffian duct (WD). Proper coiling of the epididymis is essential for male fertility, as sperm in the testis are unable to fertilize an oocyte. However, the mechanism responsible for epididymal development and coiling remains unclear, partially due to the lack of whole organ culture and imaging methods. In this study, we describe an in vitro culture system and whole mount immunofluorescence protocol to better visualize the process of WD coiling and development, which may also be applied to study other tubular organs.
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Affiliation(s)
- Manish Kumar
- Gynaecology Oncology Group, School of Biomedical Sciences and Pharmacy, University of Newcastle
| | - Pradeep Tanwar
- Gynaecology Oncology Group, School of Biomedical Sciences and Pharmacy, University of Newcastle;
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17
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Tainaka K, Kuno A, Kubota SI, Murakami T, Ueda HR. Chemical Principles in Tissue Clearing and Staining Protocols for Whole-Body Cell Profiling. Annu Rev Cell Dev Biol 2016; 32:713-741. [DOI: 10.1146/annurev-cellbio-111315-125001] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kazuki Tainaka
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan
| | - Akihiro Kuno
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
- PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Shimpei I. Kubota
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan
| | - Tatzya Murakami
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka 565-0871, Japan;
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18
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Jensen KHR, Berg RW. CLARITY-compatible lipophilic dyes for electrode marking and neuronal tracing. Sci Rep 2016; 6:32674. [PMID: 27597115 PMCID: PMC5011694 DOI: 10.1038/srep32674] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 05/10/2016] [Indexed: 12/21/2022] Open
Abstract
Fluorescent lipophilic dyes, such as DiI, stain cellular membranes and are used extensively for retrograde/anterograde labeling of neurons as well as for marking the position of extracellular electrodes after electrophysiology. Convenient histological clearing techniques, such as CLARITY, enable immunostaining and imaging of large volumes for 3D-reconstruction. However, such clearing works by removing lipids and, as an unintended consequence, also removes lipophilic dyes. To remedy this wash-out, the molecular structure of the dye can be altered to adhere to both membranes and proteins so the dye remains in the tissue after lipid–clearing. Nevertheless, the capacity of such modified dyes to remain in tissue has not yet been tested. Here, we test dyes with molecular modifications that make them aldehyde-fixable to proteins. We use three Dil–analogue dyes, CM-DiI, SP-DiI and FM 1–43FX that are modified to be CLARITY-compatible candidates. We use the challenging adult, myelin-rich spinal cord tissue, which requires prolonged lipid–clearing, of rats and mice. All three dyes remained in the tissue after lipid–clearing, but CM-DiI had the sharpest and FM 1–43FX the strongest fluorescent signal.
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Affiliation(s)
- Kristian H R Jensen
- University of Copenhagen, Department of Neuroscience and Pharmacology, Copenhagen, DK-2200, Denmark
| | - Rune W Berg
- University of Copenhagen, Department of Neuroscience and Pharmacology, Copenhagen, DK-2200, Denmark
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19
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Hirashima T. Mathematical study on robust tissue pattern formation in growing epididymal tubule. J Theor Biol 2016; 407:71-80. [PMID: 27396360 DOI: 10.1016/j.jtbi.2016.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 07/05/2016] [Indexed: 11/27/2022]
Abstract
Tissue pattern formation during development is a reproducible morphogenetic process organized by a series of kinetic cellular activities, leading to the building of functional and stable organs. Recent studies focusing on mechanical aspects have revealed physical mechanisms on how the cellular activities contribute to the formation of reproducible tissue patterns; however, the understanding for what factors achieve the reproducibility of such patterning and how it occurs is far from complete. Here, I focus on a tube pattern formation during murine epididymal development, and show that two factors influencing physical design for the patterning, the proliferative zone within the tubule and the viscosity of tissues surrounding to the tubule, control the reproducibility of epididymal tubule pattern, using a mathematical model based on experimental data. Extensive numerical simulation of the simple mathematical model revealed that a spatially localized proliferative zone within the tubule, observed in experiments, results in more reproducible tubule pattern. Moreover, I found that the viscosity of tissues surrounding to the tubule imposes a trade-off regarding pattern reproducibility and spatial accuracy relating to the region where the tubule pattern is formed. This indicates an existence of optimality in material properties of tissues for the robust patterning of epididymal tubule. The results obtained by numerical analysis based on experimental observations provide a general insight on how physical design realizes robust tissue pattern formation.
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Affiliation(s)
- Tsuyoshi Hirashima
- Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan.
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20
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Susaki E, Ueda H. Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals. Cell Chem Biol 2016; 23:137-157. [DOI: 10.1016/j.chembiol.2015.11.009] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 11/20/2015] [Accepted: 11/20/2015] [Indexed: 12/29/2022]
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