1
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Suh J, Liu Y, Smith J, Watanabe M, Rollins AM, Jenkins MW. A Simple and Fast Optical Clearing Method for Whole-Mount Fluorescence In Situ Hybridization (FISH) Imaging. JOURNAL OF BIOPHOTONICS 2024:e202400258. [PMID: 39389582 DOI: 10.1002/jbio.202400258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 09/12/2024] [Accepted: 09/16/2024] [Indexed: 10/12/2024]
Abstract
We report a single-step optical clearing method that is compatible with RNA fluorescence in situ hybridization (FISH) imaging. We previously demonstrated microscopy imaging with immunohistochemistry and genetic reporters using a technique called lipid-preserving refractive index matching for prolonged imaging depth (LIMPID). Our protocol reliably produces high-resolution three-dimensional (3D) images with minimal aberrations using high magnification objectives, captures large field-of-view images of whole-mount tissues, and supports co-labeling with antibody and FISH probes. We also custom-designed FISH probes for quail embryos, demonstrating the ease of fabricating probes for use with less common animal models. Furthermore, we show high-quality 3D images using a conventional fluorescence microscope, without using more advanced depth sectioning instruments such as confocal or light-sheet microscopy. For broader adoption, we simplified and optimized 3D-LIMPID-FISH to minimize the barrier to entry, and we provide a detailed protocol to aid users with navigating the thick and thin of 3D microscopy.
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Affiliation(s)
- Junwoo Suh
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yehe Liu
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jordan Smith
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Michiko Watanabe
- Department of Pediatrics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Andrew M Rollins
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Michael W Jenkins
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pediatrics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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2
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Zhou L, Shi W, Fu S, Li M, Chen J, Fang K, Li Y. High Refractive Index Imaging Buffer for Dual-Color 3D SMLM Imaging of Thick Samples. Anal Chem 2024; 96:15648-15656. [PMID: 39298273 DOI: 10.1021/acs.analchem.4c02893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
The current limitations of single-molecule localization microscopy (SMLM) in deep tissue imaging, primarily due to depth-dependent aberrations caused by refractive index (RI) mismatch, present a significant challenge in achieving high-resolution images at greater depths. To extend the imaging depth, we optimized the imaging buffer of SMLM with the RI matched to that of the objective immersion medium and systematically evaluated five different RI-matched buffers, focusing on their impact on the blinking behavior of red-absorbing dyes and the quality of reconstructed super-resolution images. Particularly, we found that clear unobstructed brain imaging cocktails-based imaging buffer could match the RI of oil and was able to clear the tissue samples. With the help of the RI-matched imaging buffers, we showed high-quality dual-color 3D SMLM images with imaging depths ranging from a few micrometers to tens of micrometers in both cultured cells and sectioned tissue samples. This advancement offers a practical and accessible method for high-resolution imaging at greater depths without the need for specialized optical equipment or expertise.
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Affiliation(s)
- Lulu Zhou
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wei Shi
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shuang Fu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Mengfan Li
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jianwei Chen
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ke Fang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yiming Li
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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3
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Shih CP, Tang WC, Chen P, Chen BC. Applications of Lightsheet Fluorescence Microscopy by High Numerical Aperture Detection Lens. J Phys Chem B 2024; 128:8273-8289. [PMID: 39177503 PMCID: PMC11382282 DOI: 10.1021/acs.jpcb.4c01721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
This Review explores the evolution, improvements, and recent applications of Light Sheet Fluorescence Microscopy (LSFM) in biological research using a high numerical aperture detection objective (lens) for imaging subcellular structures. The Review begins with an overview of the development of LSFM, tracing its evolution from its inception to its current state and emphasizing key milestones and technological advancements over the years. Subsequently, we will discuss various improvements of LSFM techniques, covering advancements in hardware such as illumination strategies, optical designs, and sample preparation methods that have enhanced imaging capabilities and resolution. The advancements in data acquisition and processing are also included, which provides a brief overview of the recent development of artificial intelligence. Fluorescence probes that were commonly used in LSFM will be highlighted, together with some insights regarding the selection of potential probe candidates for future LSFM development. Furthermore, we also discuss recent advances in the application of LSFM with a focus on high numerical aperture detection objectives for various biological studies. For sample preparation techniques, there are discussions regarding fluorescence probe selection, tissue clearing protocols, and some insights into expansion microscopy. Integrated setups such as adaptive optics, single objective modification, and microfluidics will also be some of the key discussion points in this Review. We hope that this comprehensive Review will provide a holistic perspective on the historical development, technical enhancements, and cutting-edge applications of LSFM, showcasing its pivotal role and future potential in advancing biological research.
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Affiliation(s)
- Chun-Pei Shih
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106319, Taiwan
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan University, Taipei 11529, Taiwan
| | - Wei-Chun Tang
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Peilin Chen
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
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4
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Leiwe MN, Fujimoto S, Baba T, Moriyasu D, Saha B, Sakaguchi R, Inagaki S, Imai T. Automated neuronal reconstruction with super-multicolour Tetbow labelling and threshold-based clustering of colour hues. Nat Commun 2024; 15:5279. [PMID: 38918382 PMCID: PMC11199630 DOI: 10.1038/s41467-024-49455-y] [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: 11/10/2022] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
Fluorescence imaging is widely used for the mesoscopic mapping of neuronal connectivity. However, neurite reconstruction is challenging, especially when neurons are densely labelled. Here, we report a strategy for the fully automated reconstruction of densely labelled neuronal circuits. Firstly, we establish stochastic super-multicolour labelling with up to seven different fluorescent proteins using the Tetbow method. With this method, each neuron is labelled with a unique combination of fluorescent proteins, which are then imaged and separated by linear unmixing. We also establish an automated neurite reconstruction pipeline based on the quantitative analysis of multiple dyes (QDyeFinder), which identifies neurite fragments with similar colour combinations. To classify colour combinations, we develop unsupervised clustering algorithm, dCrawler, in which data points in multi-dimensional space are clustered based on a given threshold distance. Our strategy allows the reconstruction of neurites for up to hundreds of neurons at the millimetre scale without using their physical continuity.
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Affiliation(s)
- Marcus N Leiwe
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- MetaCell LCC, LTD, Cambridge, MA, USA
| | - Satoshi Fujimoto
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Toshikazu Baba
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Daichi Moriyasu
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Biswanath Saha
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Richi Sakaguchi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shigenori Inagaki
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Imai
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
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5
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Miyashiro D, Tojima T, Nakano A. Extremely high spatiotemporal resolution microscopy for live cell imaging by single photon counting, noise elimination, and a novel restoration algorithm based on probability calculation. Front Cell Dev Biol 2024; 12:1324906. [PMID: 38979036 PMCID: PMC11228276 DOI: 10.3389/fcell.2024.1324906] [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: 10/20/2023] [Accepted: 06/03/2024] [Indexed: 07/10/2024] Open
Abstract
Optical microscopy is essential for direct observation of dynamic phenomena in living cells. According to the classic optical theories, the images obtained through light microscopes are blurred for about half the wavelength of light, and therefore small structures below this "diffraction limit" were thought unresolvable by conventional optical microscopy. In reality, accurately obtained optical images contain complete information about the observed objects. Temporal resolution is also important for the observation of dynamic phenomena. A challenge exists here to overcome the trade-off between the time required for measurement and the accuracy of the measurement. The present paper describes a concrete methodology for reconstructing the structure of an observed object, based on the information contained in the image obtained by optical microscopy. It is realized by accurate single photon counting, complete noise elimination, and a novel restoration algorithm based on probability calculation. This method has been implemented in the Super-resolution Confocal Live Imaging Microscopy (SCLIM) we developed. The new system named SCLIM2M achieves unprecedented high spatiotemporal resolution. We have succeeded in capturing sub-diffraction-limit structures with millisecond-level dynamics of organelles and vesicles in living cells, which were never observed by conventional optical microscopy. Actual examples of the high-speed and high-resolution 4D observation of living cells are presented.
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Affiliation(s)
- Daisuke Miyashiro
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
| | - Takuro Tojima
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
| | - Akihiko Nakano
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
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Otomo K, Omura T, Nozawa Y, Edwards SJ, Sato Y, Saito Y, Yagishita S, Uchida H, Watakabe Y, Naitou K, Yanai R, Sahara N, Takagi S, Katayama R, Iwata Y, Shiokawa T, Hayakawa Y, Otsuka K, Watanabe-Takano H, Haneda Y, Fukuhara S, Fujiwara M, Nii T, Meno C, Takeshita N, Yashiro K, Rosales Rocabado JM, Kaku M, Yamada T, Oishi Y, Koike H, Cheng Y, Sekine K, Koga JI, Sugiyama K, Kimura K, Karube F, Kim H, Manabe I, Nemoto T, Tainaka K, Hamada A, Brismar H, Susaki EA. descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques. Nat Commun 2024; 15:4941. [PMID: 38866781 PMCID: PMC11169475 DOI: 10.1038/s41467-024-49131-1] [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: 11/06/2023] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Despite widespread adoption of tissue clearing techniques in recent years, poor access to suitable light-sheet fluorescence microscopes remains a major obstacle for biomedical end-users. Here, we present descSPIM (desktop-equipped SPIM for cleared specimens), a low-cost ($20,000-50,000), low-expertise (one-day installation by a non-expert), yet practical do-it-yourself light-sheet microscope as a solution for this bottleneck. Even the most fundamental configuration of descSPIM enables multi-color imaging of whole mouse brains and a cancer cell line-derived xenograft tumor mass for the visualization of neurocircuitry, assessment of drug distribution, and pathological examination by false-colored hematoxylin and eosin staining in a three-dimensional manner. Academically open-sourced ( https://github.com/dbsb-juntendo/descSPIM ), descSPIM allows routine three-dimensional imaging of cleared samples in minutes. Thus, the dissemination of descSPIM will accelerate biomedical discoveries driven by tissue clearing technologies.
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Affiliation(s)
- Kohei Otomo
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Takaki Omura
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Neurosurgery, University of Tokyo, Tokyo, Japan
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuki Nozawa
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan
| | - Steven J Edwards
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yukihiko Sato
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuri Saito
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shigehiro Yagishita
- Department of Pharmacology and Therapeutics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hitoshi Uchida
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yuki Watakabe
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kiyotada Naitou
- Department of Basic Veterinary Science, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Rin Yanai
- Advanced Neuroimaging Center, Institute for Quantum Medical Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Naruhiko Sahara
- Advanced Neuroimaging Center, Institute for Quantum Medical Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Satoshi Takagi
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yusuke Iwata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshiro Shiokawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kensuke Otsuka
- Biology and Environmental Chemistry Division, Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry, Chiba, Japan
| | - Haruko Watanabe-Takano
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Yuka Haneda
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Shigetomo Fukuhara
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Miku Fujiwara
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takenobu Nii
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Chikara Meno
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naoki Takeshita
- Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kenta Yashiro
- Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Juan Marcelo Rosales Rocabado
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masaru Kaku
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Tatsuya Yamada
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Yumiko Oishi
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Koike
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yinglan Cheng
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keisuke Sekine
- Laboratory of Cancer Cell Systems, National Cancer Center Research Institute, Tokyo, Japan
| | - Jun-Ichiro Koga
- The Second Department of Internal Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Kaori Sugiyama
- Institute for Advanced Research of Biosystem Dynamics, Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Kenichi Kimura
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | - Fuyuki Karube
- Lab of Histology and Cytology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Hyeree Kim
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ichiro Manabe
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomomi Nemoto
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akinobu Hamada
- Department of Pharmacology and Therapeutics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Etsuo A Susaki
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan.
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan.
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan.
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Oshiro H, Hata J, Nakashima D, Hayashi N, Haga Y, Hagiya K, Yoshimaru D, Okano H. Influence of Diffusion Time and Temperature on Restricted Diffusion Signal: A Phantom Study. Magn Reson Med Sci 2024; 23:136-145. [PMID: 36754420 PMCID: PMC11024708 DOI: 10.2463/mrms.mp.2022-0103] [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: 08/16/2022] [Accepted: 12/17/2022] [Indexed: 02/10/2023] Open
Abstract
PURPOSE Diffusion MRI is a physical measurement method that quantitatively indicates the displacement of water molecules diffusing in voxels. However, there are insufficient data to characterize the diffusion process physically in a uniform structure such as a phantom. This study investigated the transitional relationship between structure scale, temperature, and diffusion time for simple restricted diffusion using a capillary phantom. METHODS We performed diffusion-weighted pulsed-gradient stimulated-echo acquisition mode (STEAM) MRI with a 9.4 Tesla MRI system (Bruker BioSpin, Ettlingen, Germany) and a quadrature coil with an inner diameter of 86 mm (Bruker BioSpin). We measured the diffusion coefficients (radial diffusivity [RD]) of capillary plates (pore sizes 6, 12, 25, 50, and 100 μm) with uniformly restricted structures at various temperatures (10ºC, 20ºC, 30ºC, and 40ºC) and multiple diffusion times (12-800 ms). We evaluated the characteristics of scale, temperature, and diffusion time for restricted diffusion. RESULTS The RD decayed and became constant depending on the structural scale. Diffusion coefficient fluctuations with temperature occurred mostly under conditions of a large structural scale and short diffusion time. We obtained data suggesting that temperature-dependent changes in the diffusion coefficients follow physical laws. CONCLUSION No water molecules were observed outside the glass tubes in the capillary plates, and the capillary plates only reflected a restricted diffusion process within the structure.We experimentally evaluated the characteristics of simple restricted diffusion to reveal the transitional relationship of the diffusion coefficient with diffusion time, structure scale, and temperature through composite measurement.
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Affiliation(s)
- Hinako Oshiro
- Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Center for Brain Science, RIKEN, Wako, Saitama, Japan
| | - Junichi Hata
- Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Center for Brain Science, RIKEN, Wako, Saitama, Japan
- School of Medicine, Keio University, Tokyo, Japan
- Division of Regenerative Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | | | - Naoya Hayashi
- Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Center for Brain Science, RIKEN, Wako, Saitama, Japan
| | - Yawara Haga
- Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Center for Brain Science, RIKEN, Wako, Saitama, Japan
| | - Kei Hagiya
- Center for Brain Science, RIKEN, Wako, Saitama, Japan
| | - Daisuke Yoshimaru
- Center for Brain Science, RIKEN, Wako, Saitama, Japan
- School of Medicine, Keio University, Tokyo, Japan
- Division of Regenerative Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Hideyuki Okano
- Center for Brain Science, RIKEN, Wako, Saitama, Japan
- School of Medicine, Keio University, Tokyo, Japan
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8
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Martínez-Torres D, Maldonado V, Pérez-Gallardo C, Yañez R, Candia V, Kalaidzidis Y, Zerial M, Morales-Navarrete H, Segovia-Miranda F. Phenotypic characterization of liver tissue heterogeneity through a next-generation 3D single-cell atlas. Sci Rep 2024; 14:2823. [PMID: 38307948 PMCID: PMC10837128 DOI: 10.1038/s41598-024-53309-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 01/30/2024] [Indexed: 02/04/2024] Open
Abstract
Three-dimensional (3D) geometrical models are potent tools for quantifying complex tissue features and exploring structure-function relationships. However, these models are generally incomplete due to experimental limitations in acquiring multiple (> 4) fluorescent channels in thick tissue sections simultaneously. Indeed, predictive geometrical and functional models of the liver have been restricted to few tissue and cellular components, excluding important cellular populations such as hepatic stellate cells (HSCs) and Kupffer cells (KCs). Here, we combined deep-tissue immunostaining, multiphoton microscopy, deep-learning techniques, and 3D image processing to computationally expand the number of simultaneously reconstructed tissue structures. We then generated a spatial single-cell atlas of hepatic architecture (Hep3D), including all main tissue and cellular components at different stages of post-natal development in mice. We used Hep3D to quantitatively study 1) hepatic morphodynamics from early post-natal development to adulthood, and 2) the effect on the liver's overall structure when changing the hepatic environment after removing KCs. In addition to a complete description of bile canaliculi and sinusoidal network remodeling, our analysis uncovered unexpected spatiotemporal patterns of non-parenchymal cells and hepatocytes differing in size, number of nuclei, and DNA content. Surprisingly, we found that the specific depletion of KCs results in morphological changes in hepatocytes and HSCs. These findings reveal novel characteristics of liver heterogeneity and have important implications for both the structural organization of liver tissue and its function. Our next-gen 3D single-cell atlas is a powerful tool to understand liver tissue architecture, opening up avenues for in-depth investigations into tissue structure across both normal and pathological conditions.
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Affiliation(s)
- Dilan Martínez-Torres
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Valentina Maldonado
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Cristian Pérez-Gallardo
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Rodrigo Yañez
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Valeria Candia
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Hernán Morales-Navarrete
- Department of Systems Biology of Development, University of Konstanz, Konstanz, Germany.
- Facultad de Ciencias Técnicas, Universidad Internacional Del Ecuador UIDE, Quito, Ecuador.
| | - Fabián Segovia-Miranda
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile.
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile.
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9
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Yamada H, Makino SI, Okunaga I, Miyake T, Yamamoto-Nonaka K, Oliva Trejo JA, Tominaga T, Empitu MA, Kadariswantiningsih IN, Kerever A, Komiya A, Ichikawa T, Arikawa-Hirasawa E, Yanagita M, Asanuma K. Beyond 2D: A scalable and highly sensitive method for a comprehensive 3D analysis of kidney biopsy tissue. PNAS NEXUS 2024; 3:pgad433. [PMID: 38193136 PMCID: PMC10772983 DOI: 10.1093/pnasnexus/pgad433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 11/06/2023] [Indexed: 01/10/2024]
Abstract
The spatial organization of various cell populations is critical for the major physiological and pathological processes in the kidneys. Most evaluation of these processes typically comes from a conventional 2D tissue cross-section, visualizing a limited amount of cell organization. Therefore, the 2D analysis of kidney biopsy introduces selection bias. The 2D analysis potentially omits key pathological findings outside a 1- to 10-μm thin-sectioned area and lacks information on tissue organization, especially in a particular irregular structure such as crescentic glomeruli. In this study, we introduce an easy-to-use and scalable method for obtaining high-quality images of molecules of interest in a large tissue volume, enabling a comprehensive evaluation of the 3D organization and cellular composition of kidney tissue, especially the glomerular structure. We show that CUBIC and ScaleS clearing protocols could allow a 3D analysis of the kidney tissues in human and animal models of kidney disease. We also demonstrate that the paraffin-embedded human biopsy specimens previously examined via 2D evaluation could be applicable to 3D analysis, showing a potential utilization of this method in kidney biopsy tissue collected in the past. In summary, the 3D analysis of kidney biopsy provides a more comprehensive analysis and a minimized selection bias than 2D tissue analysis. Additionally, this method enables a quantitative evaluation of particular kidney structures and their surrounding tissues, with the potential utilization from basic science investigation to applied diagnostics in nephrology.
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Affiliation(s)
- Hiroyuki Yamada
- Department of Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Department of Primary Care and Emergency, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Shin-ichi Makino
- Department of Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Issei Okunaga
- Department of Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Takafumi Miyake
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Kanae Yamamoto-Nonaka
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Juan Alejandro Oliva Trejo
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
| | - Takahiro Tominaga
- Department of Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Maulana A Empitu
- Department of Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | | | - Aurelien Kerever
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Akira Komiya
- Department of Urology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Tomohiko Ichikawa
- Department of Urology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Eri Arikawa-Hirasawa
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Motoko Yanagita
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8303, Japan
| | - Katsuhiko Asanuma
- Department of Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
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10
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Jiang T, Gong H, Yuan J. Whole-brain Optical Imaging: A Powerful Tool for Precise Brain Mapping at the Mesoscopic Level. Neurosci Bull 2023; 39:1840-1858. [PMID: 37715920 PMCID: PMC10661546 DOI: 10.1007/s12264-023-01112-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/08/2023] [Indexed: 09/18/2023] Open
Abstract
The mammalian brain is a highly complex network that consists of millions to billions of densely-interconnected neurons. Precise dissection of neural circuits at the mesoscopic level can provide important structural information for understanding the brain. Optical approaches can achieve submicron lateral resolution and achieve "optical sectioning" by a variety of means, which has the natural advantage of allowing the observation of neural circuits at the mesoscopic level. Automated whole-brain optical imaging methods based on tissue clearing or histological sectioning surpass the limitation of optical imaging depth in biological tissues and can provide delicate structural information in a large volume of tissues. Combined with various fluorescent labeling techniques, whole-brain optical imaging methods have shown great potential in the brain-wide quantitative profiling of cells, circuits, and blood vessels. In this review, we summarize the principles and implementations of various whole-brain optical imaging methods and provide some concepts regarding their future development.
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Affiliation(s)
- Tao Jiang
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
| | - Hui Gong
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jing Yuan
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
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11
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Delage E, Guilbert T, Yates F. Successful 3D imaging of cleared biological samples with light sheet fluorescence microscopy. J Cell Biol 2023; 222:e202307143. [PMID: 37847528 PMCID: PMC10583220 DOI: 10.1083/jcb.202307143] [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: 07/28/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023] Open
Abstract
In parallel with the development of tissue-clearing methods, over the last decade, light sheet fluorescence microscopy has contributed to major advances in various fields, such as cell and developmental biology and neuroscience. While biologists are increasingly integrating three-dimensional imaging into their research projects, their experience with the technique is not always up to their expectations. In response to a survey of specific challenges associated with sample clearing and labeling, image acquisition, and data analysis, we have critically assessed the recent literature to characterize the difficulties inherent to light sheet fluorescence microscopy applied to cleared biological samples and to propose solutions to overcome them. This review aims to provide biologists interested in light sheet fluorescence microscopy with a primer for the development of their imaging pipeline, from sample preparation to image analysis. Importantly, we believe that issues could be avoided with better anticipation of image analysis requirements, which should be kept in mind while optimizing sample preparation and acquisition parameters.
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Affiliation(s)
- Elise Delage
- CellTechs Laboratory, SupBiotech, Villejuif, France
- Service d’Etude des Prions et des Infections Atypiques, Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives, Université Paris Saclay, Fontenay-aux-Roses, France
| | - Thomas Guilbert
- Institut Cochin, Institut national de la santé et de la recherche médicale (U1016), Centre National de la Recherche Scientifique (UMR 8104), Université de Paris (UMR-S1016), Paris, France
| | - Frank Yates
- CellTechs Laboratory, SupBiotech, Villejuif, France
- Service d’Etude des Prions et des Infections Atypiques, Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives, Université Paris Saclay, Fontenay-aux-Roses, France
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12
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Niiyama T, Fujimoto S, Imai T. Microglia Are Dispensable for Developmental Dendrite Pruning of Mitral Cells in Mice. eNeuro 2023; 10:ENEURO.0323-23.2023. [PMID: 37890992 PMCID: PMC10644373 DOI: 10.1523/eneuro.0323-23.2023] [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: 08/26/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023] Open
Abstract
During early development, neurons in the brain often form excess synaptic connections. Later, they strengthen some connections while eliminating others to build functional neuronal circuits. In the olfactory bulb, a mitral cell initially extends multiple dendrites to multiple glomeruli but eventually forms a single primary dendrite through the activity-dependent dendrite pruning process. Recent studies have reported that microglia facilitate synapse pruning during the circuit remodeling in some systems. It has remained unclear whether microglia are involved in the activity-dependent dendrite pruning in the developing brains. Here, we examined whether microglia are required for the developmental dendrite pruning of mitral cells in mice. To deplete microglia in the fetal brain, we treated mice with a colony-stimulating factor 1 receptor (CSF1R) inhibitor, PLX5622, from pregnancy. Microglia were reduced by >90% in mice treated with PLX5622. However, dendrite pruning of mitral cells was not significantly affected. Moreover, we found no significant differences in the number, density, and size of excitatory synapses formed in mitral cell dendrites. We also found no evidence for the role of microglia in the activity-dependent dendrite remodeling of layer 4 (L4) neurons in the barrel cortex. In contrast, the density of excitatory synapses (dendritic spines) in granule cells in the olfactory bulb was significantly increased in mice treated with PLX5622 at postnatal day (P) 6, suggesting a role for the regulation of dendritic spines. Our results indicate that microglia do not play a critical role in activity-dependent dendrite pruning at the neurite level during early postnatal development in mice.
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Affiliation(s)
- Tetsushi Niiyama
- Graduate School of Medical Sciences, Kyushu University, 812-8582, Fukuoka, Japan
| | - Satoshi Fujimoto
- Graduate School of Medical Sciences, Kyushu University, 812-8582, Fukuoka, Japan
| | - Takeshi Imai
- Graduate School of Medical Sciences, Kyushu University, 812-8582, Fukuoka, Japan
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13
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Tsutsumi M, Takahashi T, Kobayashi K, Nemoto T. Fluorescence radial fluctuation enables two-photon super-resolution microscopy. Front Cell Neurosci 2023; 17:1243633. [PMID: 37881492 PMCID: PMC10595032 DOI: 10.3389/fncel.2023.1243633] [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: 06/21/2023] [Accepted: 09/26/2023] [Indexed: 10/27/2023] Open
Abstract
Despite recent improvements in microscopy, it is still difficult to apply super-resolution microscopy for deep imaging due to the deterioration of light convergence properties in thick specimens. As a strategy to avoid such optical limitations for deep super-resolution imaging, we focused on super-resolution radial fluctuation (SRRF), a super-resolution technique based on image analysis. In this study, we applied SRRF to two-photon microscopy (2P-SRRF) and characterized its spatial resolution, suitability for deep observation, and morphological reproducibility in real brain tissue. By the comparison with structured illumination microscopy (SIM), it was confirmed that 2P-SRRF exhibited two-point resolution and morphological reproducibility comparable to that of SIM. The improvement in spatial resolution was also demonstrated at depths of more than several hundred micrometers in a brain-mimetic environment. After optimizing SRRF processing parameters, we successfully demonstrated in vivo high-resolution imaging of the fifth layer of the cerebral cortex using 2P-SRRF. This is the first report on the application of SRRF to in vivo two-photon imaging. This method can be easily applied to existing two-photon microscopes and can expand the visualization range of super-resolution imaging studies.
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Affiliation(s)
- Motosuke Tsutsumi
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
- Research Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
| | - Taiga Takahashi
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
- Research Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kentaro Kobayashi
- Nikon Imaging Center, Research Institute for Electronic Science, Hokkaido University, Sapporo, Japan
| | - Tomomi Nemoto
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
- Research Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Nikon Imaging Center, Research Institute for Electronic Science, Hokkaido University, Sapporo, Japan
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14
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Unterweger IA, Klepstad J, Hannezo E, Lundegaard PR, Trusina A, Ober EA. Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics. PLoS Biol 2023; 21:e3002315. [PMID: 37792696 PMCID: PMC10550115 DOI: 10.1371/journal.pbio.3002315] [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: 01/18/2023] [Accepted: 08/29/2023] [Indexed: 10/06/2023] Open
Abstract
To meet the physiological demands of the body, organs need to establish a functional tissue architecture and adequate size as the embryo develops to adulthood. In the liver, uni- and bipotent progenitor differentiation into hepatocytes and biliary epithelial cells (BECs), and their relative proportions, comprise the functional architecture. Yet, the contribution of individual liver progenitors at the organ level to both fates, and their specific proportion, is unresolved. Combining mathematical modelling with organ-wide, multispectral FRaeppli-NLS lineage tracing in zebrafish, we demonstrate that a precise BEC-to-hepatocyte ratio is established (i) fast, (ii) solely by heterogeneous lineage decisions from uni- and bipotent progenitors, and (iii) independent of subsequent cell type-specific proliferation. Extending lineage tracing to adulthood determined that embryonic cells undergo spatially heterogeneous three-dimensional growth associated with distinct environments. Strikingly, giant clusters comprising almost half a ventral lobe suggest lobe-specific dominant-like growth behaviours. We show substantial hepatocyte polyploidy in juveniles representing another hallmark of postembryonic liver growth. Our findings uncover heterogeneous progenitor contributions to tissue architecture-defining cell type proportions and postembryonic organ growth as key mechanisms forming the adult liver.
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Affiliation(s)
- Iris. A. Unterweger
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem), Copenhagen N, Denmark
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen N, Denmark
| | - Julie Klepstad
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
- Andalusian Center for Developmental Biology, CSIC, University Pablo de Olavide, Seville, Spain
| | - Edouard Hannezo
- Institute of Science and Technology, Klosterneuburg, Austria
| | - Pia R. Lundegaard
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen N, Denmark
| | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Elke A. Ober
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem), Copenhagen N, Denmark
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen N, Denmark
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15
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Tanaka K, Kawai S, Fujii E, Yano M, Miyayama T, Nakano K, Terao K, Suzuki M. Development of rat duodenal monolayer model with effective barrier function from rat organoids for ADME assay. Sci Rep 2023; 13:12130. [PMID: 37495742 PMCID: PMC10372144 DOI: 10.1038/s41598-023-39425-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023] Open
Abstract
The in-depth analysis of the ADME profiles of drug candidates using in vitro models is essential for drug development since a drug's exposure in humans depends on its ADME properties. In contrast to efforts in developing human in vitro absorption models, only a limited number of studies have explored models using rats, the most frequently used species in in vivo DMPK studies. In this study, we developed a monolayer model with an effective barrier function for ADME assays using rat duodenal organoids as a cell source. At first, we developed rat duodenal organoids according to a previous report, but they were not able to generate a confluent monolayer. Therefore, we modified organoid culture protocols and developed cyst-enriched organoids; these strongly promoted the formation of a confluent monolayer. Furthermore, adding valproic acid to the culture accelerated the differentiation of the monolayer, which possessed an effective barrier function and apicobasal cell polarity. Drug transporter P-gp function as well as CYP3A activity and nuclear receptor function were confirmed in the model. We expect our novel monolayer model to be a useful tool for elucidating drug absorption processes in detail, enabling the development of highly absorbable drugs.
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Affiliation(s)
- Kai Tanaka
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 5-1-1 Tsukiji Chuo-Ku, Tokyo, 104-0045, Japan.
| | - Shigeto Kawai
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 5-1-1 Tsukiji Chuo-Ku, Tokyo, 104-0045, Japan
| | - Etsuko Fujii
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 216 Totsuka Totsuka-Ku Yokohama, Kanagawa, 244-8602, Japan
| | - Masumi Yano
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 216 Totsuka Totsuka-Ku Yokohama, Kanagawa, 244-8602, Japan
| | - Takashi Miyayama
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 216 Totsuka Totsuka-Ku Yokohama, Kanagawa, 244-8602, Japan
| | - Kiyotaka Nakano
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 5-1-1 Tsukiji Chuo-Ku, Tokyo, 104-0045, Japan
| | - Kimio Terao
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., 2-1-1 Nihonbashi-Muromachi Chuo-Ku, Tokyo, 103-8324, Japan
| | - Masami Suzuki
- Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka, 412-8513, Japan
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16
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Kato Y, Saga Y. Antagonism between DDX6 and PI3K-AKT signaling is an oocyte-intrinsic mechanism controlling primordial follicle growth†. Biol Reprod 2023; 109:73-82. [PMID: 37067907 DOI: 10.1093/biolre/ioad043] [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: 02/01/2023] [Revised: 04/03/2023] [Accepted: 04/12/2023] [Indexed: 04/18/2023] Open
Abstract
Oocyte maturation and subsequent ovulation during the reproductive lifespan ensure long-term reproduction in mammalian females. This is achieved by tight regulation for the maintenance and growth of primordial follicles. However, the underlying mechanisms remain unsolved. We herein report that posttranscriptional gene regulation mediated by an RNA helicase, DEAD-box helicase 6 (DDX6), and phosphoinositide-3-kinase (PI3K)-AKT signaling exhibits an antagonistic interaction in mouse primordial follicles. DDX6 forms P-body-like cytoplasmic foci in oocytes, which colocalize to a P-body component, DCP1A. Interestingly, the P-body-like granules predominantly assemble in primordial follicles, but disperse once follicle growth is initiated, suggesting that they play a role in the maintenance of primordial follicles. Oocyte-specific knockout of Ddx6 using Gdf9-iCre revealed that Ddx6-deficient oocytes are defective in foci assembly and are abnormally enlarged, resulting in premature depletion of primordial follicles. These results indicate that DDX6 is required to maintain primordial follicles. The abnormal oocyte enlargement is because of enhanced PI3K-AKT signaling, a pivotal signaling pathway in the growth of primordial follicles. Conversely, the forced activation of PI3K-AKT signaling by knocking out Pten disassembles P-body-like granules in primordial follicles. These data suggest that DDX6 and PI3K-AKT signaling mutually antagonize the assembly of P-body-like granules and the growth of primordial follicles. We propose this mutual antagonism as an oocyte-intrinsic mechanism controlling the maintenance and growth of primordial follicles, ensuring the longevity of female reproduction.
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Affiliation(s)
- Yuzuru Kato
- Department of Gene Function and Phenomics, Mammalian Development Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Yumiko Saga
- Department of Gene Function and Phenomics, Mammalian Development Laboratory, National Institute of Genetics, Shizuoka, Japan
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17
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Obi-Nagata K, Suzuki N, Miyake R, MacDonald ML, Fish KN, Ozawa K, Nagahama K, Okimura T, Tanaka S, Kano M, Fukazawa Y, Sweet RA, Hayashi-Takagi A. Distorted neurocomputation by a small number of extra-large spines in psychiatric disorders. SCIENCE ADVANCES 2023; 9:eade5973. [PMID: 37294752 PMCID: PMC10256173 DOI: 10.1126/sciadv.ade5973] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/05/2023] [Indexed: 06/11/2023]
Abstract
Human genetics strongly support the involvement of synaptopathy in psychiatric disorders. However, trans-scale causality linking synapse pathology to behavioral changes is lacking. To address this question, we examined the effects of synaptic inputs on dendrites, cells, and behaviors of mice with knockdown of SETD1A and DISC1, which are validated animal models of schizophrenia. Both models exhibited an overrepresentation of extra-large (XL) synapses, which evoked supralinear dendritic and somatic integration, resulting in increased neuronal firing. The probability of XL spines correlated negatively with working memory, and the optical prevention of XL spine generation restored working memory impairment. Furthermore, XL synapses were more abundant in the postmortem brains of patients with schizophrenia than in those of matched controls. Our findings suggest that working memory performance, a pivotal aspect of psychiatric symptoms, is shaped by distorted dendritic and somatic integration via XL spines.
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Affiliation(s)
- Kisho Obi-Nagata
- Laboratory for Multi-scale Biological Psychiatry, Center for Brain Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0106, Japan
- Gunma University Graduate School of Medicine, Maebashi City, Gunma 371-8512, Japan
| | - Norimitsu Suzuki
- Laboratory for Multi-scale Biological Psychiatry, Center for Brain Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0106, Japan
| | - Ryuhei Miyake
- Laboratory for Multi-scale Biological Psychiatry, Center for Brain Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0106, Japan
| | - Matthew L. MacDonald
- Departments of Psychiatry, Neurology, Statistics, and Neurobiology, Translational Neuroscience Program, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Kenneth N. Fish
- Departments of Psychiatry, Neurology, Statistics, and Neurobiology, Translational Neuroscience Program, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Katsuya Ozawa
- Laboratory for Multi-scale Biological Psychiatry, Center for Brain Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0106, Japan
| | - Kenichiro Nagahama
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
| | - Tsukasa Okimura
- Medical Institute of Developmental Disabilities Research, Showa University, Tokyo 157-8577, Japan
| | - Shoji Tanaka
- Department of Information and Communication Sciences, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Masanobu Kano
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
| | - Yugo Fukazawa
- Division of Brain Structure and Function, Faculty of Medical Science, University of Fukui, Yoshida, Fukui, 910-1193, Japan
| | - Robert A. Sweet
- Departments of Psychiatry, Neurology, Statistics, and Neurobiology, Translational Neuroscience Program, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Akiko Hayashi-Takagi
- Laboratory for Multi-scale Biological Psychiatry, Center for Brain Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0106, Japan
- Gunma University Graduate School of Medicine, Maebashi City, Gunma 371-8512, Japan
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18
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Manubens-Gil L, Zhou Z, Chen H, Ramanathan A, Liu X, Liu Y, Bria A, Gillette T, Ruan Z, Yang J, Radojević M, Zhao T, Cheng L, Qu L, Liu S, Bouchard KE, Gu L, Cai W, Ji S, Roysam B, Wang CW, Yu H, Sironi A, Iascone DM, Zhou J, Bas E, Conde-Sousa E, Aguiar P, Li X, Li Y, Nanda S, Wang Y, Muresan L, Fua P, Ye B, He HY, Staiger JF, Peter M, Cox DN, Simonneau M, Oberlaender M, Jefferis G, Ito K, Gonzalez-Bellido P, Kim J, Rubel E, Cline HT, Zeng H, Nern A, Chiang AS, Yao J, Roskams J, Livesey R, Stevens J, Liu T, Dang C, Guo Y, Zhong N, Tourassi G, Hill S, Hawrylycz M, Koch C, Meijering E, Ascoli GA, Peng H. BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets. Nat Methods 2023; 20:824-835. [PMID: 37069271 DOI: 10.1038/s41592-023-01848-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 03/14/2023] [Indexed: 04/19/2023]
Abstract
BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.
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Affiliation(s)
- Linus Manubens-Gil
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Zhi Zhou
- Microsoft Corporation, Redmond, WA, USA
| | | | - Arvind Ramanathan
- Computing, Environment and Life Sciences Directorate, Argonne National Laboratory, Lemont, IL, USA
| | | | - Yufeng Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | | | - Todd Gillette
- Center for Neural Informatics, Structures and Plasticity, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA
| | - Zongcai Ruan
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Jian Yang
- Faculty of Information Technology, Beijing University of Technology, Beijing, China
- Beijing International Collaboration Base on Brain Informatics and Wisdom Services, Beijing, China
| | | | - Ting Zhao
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Li Cheng
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Lei Qu
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing, Anhui University, Hefei, China
| | | | - Kristofer E Bouchard
- Scientific Data Division and Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
- Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience, UC Berkeley, Berkeley, CA, USA
| | - Lin Gu
- RIKEN AIP, Tokyo, Japan
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo, Japan
| | - Weidong Cai
- School of Computer Science, University of Sydney, Sydney, New South Wales, Australia
| | - Shuiwang Ji
- Texas A&M University, College Station, TX, USA
| | - Badrinath Roysam
- Cullen College of Engineering, University of Houston, Houston, TX, USA
| | - Ching-Wei Wang
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Hongchuan Yu
- National Centre for Computer Animation, Bournemouth University, Poole, UK
| | | | - Daniel Maxim Iascone
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Jie Zhou
- Department of Computer Science, Northern Illinois University, DeKalb, IL, USA
| | | | - Eduardo Conde-Sousa
- i3S, Instituto de Investigação E Inovação Em Saúde, Universidade Do Porto, Porto, Portugal
- INEB, Instituto de Engenharia Biomédica, Universidade Do Porto, Porto, Portugal
| | - Paulo Aguiar
- i3S, Instituto de Investigação E Inovação Em Saúde, Universidade Do Porto, Porto, Portugal
| | - Xiang Li
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yujie Li
- Allen Institute for Brain Science, Seattle, WA, USA
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, GA, USA
| | - Sumit Nanda
- Center for Neural Informatics, Structures and Plasticity, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA
| | - Yuan Wang
- Program in Neuroscience, Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, USA
| | - Leila Muresan
- Cambridge Advanced Imaging Centre, University of Cambridge, Cambridge, UK
| | - Pascal Fua
- Computer Vision Laboratory, EPFL, Lausanne, Switzerland
| | - Bing Ye
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Hai-Yan He
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Jochen F Staiger
- Institute for Neuroanatomy, University Medical Center Göttingen, Georg-August- University Göttingen, Goettingen, Germany
| | - Manuel Peter
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Daniel N Cox
- Neuroscience Institute, Georgia State University, Atlanta, GA, USA
| | - Michel Simonneau
- 42 ENS Paris-Saclay, CNRS, CentraleSupélec, LuMIn, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Marcel Oberlaender
- Max Planck Group: In Silico Brain Sciences, Max Planck Institute for Neurobiology of Behavior - caesar, Bonn, Germany
| | - Gregory Jefferis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Kei Ito
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Institute for Quantitative Biosciences, University of Tokyo, Tokyo, Japan
- Institute of Zoology, Biocenter Cologne, University of Cologne, Cologne, Germany
| | | | - Jinhyun Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea
| | - Edwin Rubel
- Virginia Merrill Bloedel Hearing Research Center, University of Washington, Seattle, WA, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Aljoscha Nern
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Ann-Shyn Chiang
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Jane Roskams
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Zoology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rick Livesey
- Zayed Centre for Rare Disease Research, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Janine Stevens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Tianming Liu
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, GA, USA
| | - Chinh Dang
- Virginia Merrill Bloedel Hearing Research Center, University of Washington, Seattle, WA, USA
| | - Yike Guo
- Data Science Institute, Imperial College London, London, UK
| | - Ning Zhong
- Faculty of Information Technology, Beijing University of Technology, Beijing, China
- Beijing International Collaboration Base on Brain Informatics and Wisdom Services, Beijing, China
- Department of Life Science and Informatics, Maebashi Institute of Technology, Maebashi, Japan
| | | | - Sean Hill
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Erik Meijering
- School of Computer Science and Engineering, University of New South Wales, Sydney, New South Wales, Australia.
| | - Giorgio A Ascoli
- Center for Neural Informatics, Structures and Plasticity, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA.
| | - Hanchuan Peng
- Institute for Brain and Intelligence, Southeast University, Nanjing, China.
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19
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Fujimoto S, Leiwe MN, Aihara S, Sakaguchi R, Muroyama Y, Kobayakawa R, Kobayakawa K, Saito T, Imai T. Activity-dependent local protection and lateral inhibition control synaptic competition in developing mitral cells in mice. Dev Cell 2023:S1534-5807(23)00237-X. [PMID: 37290446 DOI: 10.1016/j.devcel.2023.05.004] [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: 10/04/2022] [Revised: 02/20/2023] [Accepted: 05/16/2023] [Indexed: 06/10/2023]
Abstract
In developing brains, activity-dependent remodeling facilitates the formation of precise neuronal connectivity. Synaptic competition is known to facilitate synapse elimination; however, it has remained unknown how different synapses compete with one another within a post-synaptic cell. Here, we investigate how a mitral cell in the mouse olfactory bulb prunes all but one primary dendrite during the developmental remodeling process. We find that spontaneous activity generated within the olfactory bulb is essential. We show that strong glutamatergic inputs to one dendrite trigger branch-specific changes in RhoA activity to facilitate the pruning of the remaining dendrites: NMDAR-dependent local signals suppress RhoA to protect it from pruning; however, the subsequent neuronal depolarization induces neuron-wide activation of RhoA to prune non-protected dendrites. NMDAR-RhoA signals are also essential for the synaptic competition in the mouse barrel cortex. Our results demonstrate a general principle whereby activity-dependent lateral inhibition across synapses establishes a discrete receptive field of a neuron.
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Affiliation(s)
- Satoshi Fujimoto
- Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; Laboratory for Sensory Circuit Formation, Riken Center for Developmental Biology, Kobe 650-0047, Japan
| | - Marcus N Leiwe
- Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; Laboratory for Sensory Circuit Formation, Riken Center for Developmental Biology, Kobe 650-0047, Japan
| | - Shuhei Aihara
- Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; Laboratory for Sensory Circuit Formation, Riken Center for Developmental Biology, Kobe 650-0047, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Richi Sakaguchi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; Laboratory for Sensory Circuit Formation, Riken Center for Developmental Biology, Kobe 650-0047, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Yuko Muroyama
- Department of Developmental Biology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Reiko Kobayakawa
- Institute of Biomedical Science, Kansai Medical University, Hirakata 573-1010, Japan
| | - Ko Kobayakawa
- Institute of Biomedical Science, Kansai Medical University, Hirakata 573-1010, Japan
| | - Tetsuichiro Saito
- Department of Developmental Biology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Takeshi Imai
- Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; Laboratory for Sensory Circuit Formation, Riken Center for Developmental Biology, Kobe 650-0047, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; PRESTO and CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
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20
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Waxman S, Quinn M, Donahue C, Falo LD, Sun D, Jakobs TC, Sigal IA. Individual astrocyte morphology in the collagenous lamina cribrosa revealed by multicolor DiOlistic labeling. Exp Eye Res 2023; 230:109458. [PMID: 36965593 PMCID: PMC10152998 DOI: 10.1016/j.exer.2023.109458] [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: 12/21/2022] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/27/2023]
Abstract
Astrocytes in the lamina region of the optic nerve head play vital roles in supporting retinal ganglion cell axon health. In glaucoma, these astrocytes are implicated as early responders to stressors, undergoing characteristic changes in cell function as well as cell morphology. Much of what is currently known about individual lamina astrocyte morphology has been learned from rodent models which lack a defining feature of the human optic nerve head, the collagenous lamina cribrosa (LC). Current methods available for evaluation of collagenous LC astrocyte morphology have significant shortcomings. We aimed to evaluate Multicolor DiOlistic labeling (MuDi) as an approach to reveal individual astrocyte morphologies across the collagenous LC. Gold microcarriers were coated with all combinations of three fluorescent cell membrane dyes, DiI, DiD, and DiO, for a total of seven dye combinations. Microcarriers were delivered to 150 μm-thick coronal vibratome slices through the LC of pig, sheep, goat, and monkey eyes via MuDi. Labeled tissues were imaged with confocal and second harmonic generation microscopy to visualize dyed cells and LC collagenous beams, respectively. GFAP labeling of DiOlistically-labeled cells with astrocyte morphologies was used to investigate cell identity. 3D models of astrocytes were created from confocal image stacks for quantification of morphological features. DiOlistic labeling revealed fine details of LC astrocyte morphologies including somas, primary branches, higher-order branches, and end-feet. Labeled cells with astrocyte morphologies were GFAP+. Astrocytes were visible across seven distinct color channels, allowing high labeling density while still distinguishing individual cells from their neighbors. MuDi was capable of revealing tens to hundreds of collagenous LC astrocytes, in situ, with a single application. 3D astrocyte models allowed automated quantification of morphological features including branch number, length, thickness, hierarchy, and straightness as well as Sholl analysis. MuDi labeling provides an opportunity to investigate morphologies of collagenous LC astrocytes, providing both qualitative and quantitative detail, in healthy tissues. This approach may open doors for research of glaucoma, where astrocyte morphological alterations are thought to coincide with key functional changes related to disease progression.
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Affiliation(s)
- Susannah Waxman
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marissa Quinn
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Cara Donahue
- Department of Dermatology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Louis D Falo
- Department of Dermatology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel Sun
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Tatjana C Jakobs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Ian A Sigal
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
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21
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Gu Q, Sarkar S, Raymick B, Kanungo J. Combining tissue clearing and Fluoro-Jade C labeling for neurotoxicity assessments. Exp Biol Med (Maywood) 2023; 248:605-611. [PMID: 37208909 PMCID: PMC10350804 DOI: 10.1177/15353702231165009] [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: 02/13/2023] [Accepted: 03/02/2023] [Indexed: 05/21/2023] Open
Abstract
Tissue clearing refers to laboratory methods that make tissue transparent by chemical means. This approach allows the labeling, visualization, and analysis of specific targets without cutting the tissue into sections, thereby maintaining three-dimensional architecture. More than two dozen tissue-clearing methods have been developed by different research teams to date. While tissue clearing has been successfully applied in several studies concerning basic science or diseases, little is known about the utilization of tissue clearing for neurotoxicity evaluation. In this study, several tissue-clearing methods were combined with Fluoro-Jade C (FJ-C), a standard marker of neurodegeneration. The results suggest that some but not all tissue-clearing media are compatible with the FJ-C fluorophore. By utilizing a neurotoxicity animal model, the results further suggest that FJ-C labeling can be combined with tissue clearing for neurotoxicity assessments. This approach has the potential to be expanded further by combining multicolor labeling of molecular targets involved in the development and/or mechanisms of neurotoxicity and neurodegeneration.
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Affiliation(s)
- Qiang Gu
- Division of Neurotoxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Sumit Sarkar
- Division of Neurotoxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Bryan Raymick
- Division of Neurotoxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Jyotshna Kanungo
- Division of Neurotoxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
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22
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Zhu J, Liu X, Xu J, Deng Y, Wang P, Liu Z, Yang Q, Li D, Yu T, Zhu D. A versatile vessel casting method for fine mapping of vascular networks using a hydrogel-based lipophilic dye solution. CELL REPORTS METHODS 2023; 3:100407. [PMID: 36936073 PMCID: PMC10014313 DOI: 10.1016/j.crmeth.2023.100407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/11/2022] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
Abstract
Efficient labeling of the vasculature is important for understanding the organization of vascular networks. Here, we propose VALID, a vessel-labeling method that enables visualization of vascular networks with tissue clearing and light-sheet microscopy. VALID transforms traditional lipophilic dye solution into hydrogel by introducing gelatin and restrains the dye aggregation, resulting in complete and uniform vessel-labeling patterns with high signal-to-background ratios. VALID also enhances the compatibility of lipophilic dyes with solvent-based tissue-clearing protocols, which was hard to achieve previously. Using VALID, we combined lipophilic dyes with solvent-based tissue-clearing techniques to perform 3D reconstructions of vasculature within mouse brain and spinal cord. We also employed VALID for 3D visualization and quantification of microvascular damage in a middle cerebral artery occlusion mouse model. VALID should provide a simple, cost-effective vessel-labeling protocol that would significantly widen the applications of lipophilic dyes in research on cerebrovascular complications.
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Affiliation(s)
- Jingtan Zhu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Xiaomei Liu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Jianyi Xu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yating Deng
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Pingfu Wang
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Zhang Liu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Qihang Yang
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Dongyu Li
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Tingting Yu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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23
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Sugimoto S, Kinjo Y. Instantaneous Clearing of Biofilm (iCBiofilm): an optical approach to revisit bacterial and fungal biofilm imaging. Commun Biol 2023; 6:38. [PMID: 36690667 PMCID: PMC9870912 DOI: 10.1038/s42003-022-04396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 12/21/2022] [Indexed: 01/24/2023] Open
Abstract
Whole-biofilm imaging at single-cell resolution is necessary for system-level analysis of cellular heterogeneity, identification of key matrix component functions and response to immune cells and antimicrobials. To this end, we developed a whole-biofilm clearing and imaging method, termed instantaneous clearing of biofilm (iCBiofilm). iCBiofilm is a simple, rapid, and efficient method involving the immersion of biofilm samples in a refractive index-matching medium, enabling instant whole-biofilm imaging with confocal laser scanning microscopy. We also developed non-fixing iCBiofilm, enabling live and dynamic imaging of biofilm development and actions of antimicrobials. iCBiofilm is applicable for multicolor imaging of fluorescent proteins, immunostained matrix components, and fluorescence labeled cells in biofilms with a thickness of several hundred micrometers. iCBiofilm is scalable from bacterial to fungal biofilms and can be used to observe biofilm-neutrophil interactions. iCBiofilm therefore represents an important advance for examining the dynamics and functions of biofilms and revisiting bacterial and fungal biofilm formation.
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Affiliation(s)
- Shinya Sugimoto
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.
- Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.
| | - Yuki Kinjo
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
- Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
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24
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Zhan YJ, Zhang SW, Zhu S, Jiang N. Tissue Clearing and Its Application in the Musculoskeletal System. ACS OMEGA 2023; 8:1739-1758. [PMID: 36687066 PMCID: PMC9850472 DOI: 10.1021/acsomega.2c05180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The musculoskeletal system is an integral part of the human body. Currently, most skeletal muscle research is conducted through conventional histological sections due to technological limitations and the structure of skeletal muscles. For studying and observing bones and muscles, there is an urgent need for three-dimensional, objective imaging technologies. Optical tissue-clearing technologies seem to offer a novel and accessible approach to research of the musculoskeletal system. Using this approach, the components which cause refraction or prevent light from penetrating into the tissue are physically and chemically eliminated; then the liquid in the tissue is replaced with high-refractive-index chemicals. This innovative method, which allows three-dimensional reconstruction at the cellular and subcellular scale, significantly improves imaging depth and resolution. Nonetheless, this technology was not originally developed to image bones or muscles. When compared with brain and nerve organs which have attracted considerable attention in this field, the musculoskeletal system contains fewer lipids and has high levels of hemoglobin, collagen fibers, and inorganic hydroxyapatite crystals. Currently, three-dimensional imaging methods are widely used in the diagnosis and treatment of skeletal and muscular illnesses. In this regard, it is vitally important to review and evaluate the optical tissue-clearing technologies currently employed in the musculoskeletal system, so that researchers may make an informed decision. In the meantime, this study offers guidelines and recommendations for expanding the use of this technology in the musculoskeletal system.
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Affiliation(s)
- Yan-Jing Zhan
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Shi-Wen Zhang
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - SongSong Zhu
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Nan Jiang
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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25
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Choi JE, Choi DI, Lee J, Kim J, Kim MJ, Hong I, Jung H, Sung Y, Kim JI, Kim T, Yu NK, Lee SH, Choe HK, Koo JW, Kim JH, Kaang BK. Synaptic ensembles between raphe and D 1R-containing accumbens shell neurons underlie postisolation sociability in males. SCIENCE ADVANCES 2022; 8:eabo7527. [PMID: 36223467 PMCID: PMC9555785 DOI: 10.1126/sciadv.abo7527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Social animals expend considerable energy to maintain social bonds throughout their life. Male and female mice show sexually dimorphic behaviors, yet the underlying neural mechanisms of sociability and their dysregulation during social disconnection remain unknown. Dopaminergic neurons in dorsal raphe nucleus (DRNTH) is known to contribute to a loneliness-like state and modulate sociability. We identified that activated subpopulations in DRNTH and nucleus accumbens shell (NAcsh) during 24 hours of social isolation underlie the increase in isolation-induced sociability in male but not in female mice. This effect was reversed by chemogenetically and optogenetically inhibiting the DRNTH-NAcsh circuit. Moreover, synaptic connectivity among the activated neuronal ensembles in this circuit was increased, primarily in D1 receptor-expressing neurons in NAcsh. The increase in synaptic density functionally correlated with elevated dopamine release into NAcsh. Overall, specific synaptic ensembles in DRNTH-NAcsh mediate sex differences in isolation-induced sociability, indicating that sex-dependent circuit dynamics underlie the expression of sexually dimorphic behaviors.
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Affiliation(s)
- Ja Eun Choi
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Dong Il Choi
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jisu Lee
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jooyoung Kim
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Min Jung Kim
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Ilgang Hong
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Hyunsu Jung
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Yongmin Sung
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Ji-il Kim
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - TaeHyun Kim
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Nam-Kyung Yu
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Seung-Hee Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, South Korea
| | - Han Kyoung Choe
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), 333 Technojoongang-daero, Dalseong-gun, Daegu 42988, South Korea
| | - Ja Wook Koo
- Emotion, Cognition & Behavior Research Group, Korea Brain Research Institute, 61, Cheomdan-ro, Dong-gu, Daegu 41062, South Korea
| | - Joung-Hun Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), 77, Cheongam-ro, Nam-Gu, Pohang 37673, South Korea
| | - Bong-Kiun Kaang
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
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26
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Caviglia S, Unterweger IA, Gasiūnaitė A, Vanoosthuyse AE, Cutrale F, Trinh LA, Fraser SE, Neuhauss SCF, Ober EA. FRaeppli: a multispectral imaging toolbox for cell tracing and dense tissue analysis in zebrafish. Development 2022; 149:276363. [DOI: 10.1242/dev.199615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/20/2022] [Indexed: 12/15/2022]
Abstract
ABSTRACT
Visualizing cell shapes and interactions of differentiating cells is instrumental for understanding organ development and repair. Across species, strategies for stochastic multicolour labelling have greatly facilitated in vivo cell tracking and mapping neuronal connectivity. Yet integrating multi-fluorophore information into the context of developing zebrafish tissues is challenging given their cytoplasmic localization and spectral incompatibility with common fluorescent markers. Inspired by Drosophila Raeppli, we developed FRaeppli (Fish-Raeppli) by expressing bright membrane- or nuclear-targeted fluorescent proteins for efficient cell shape analysis and tracking. High spatiotemporal activation flexibility is provided by the Gal4/UAS system together with Cre/lox and/or PhiC31 integrase. The distinct spectra of the FRaeppli fluorescent proteins allow simultaneous imaging with GFP and infrared subcellular reporters or tissue landmarks. We demonstrate the suitability of FRaeppli for live imaging of complex internal organs, such as the liver, and have tailored hyperspectral protocols for time-efficient acquisition. Combining FRaeppli with polarity markers revealed previously unknown canalicular topologies between differentiating hepatocytes, reminiscent of the mammalian liver, suggesting common developmental mechanisms. The multispectral FRaeppli toolbox thus enables the comprehensive analysis of intricate cellular morphologies, topologies and lineages at single-cell resolution in zebrafish.
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Affiliation(s)
- Sara Caviglia
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
- University of Zurich 2 , Department of Molecular and Life Sciences, Winterthurerstrasse 190, 8057 Zürich , Switzerland
| | - Iris A. Unterweger
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
| | - Akvilė Gasiūnaitė
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
| | - Alexandre E. Vanoosthuyse
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California 3 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- Biomedical Engineering, University of Southern California 4 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
| | - Le A. Trinh
- Translational Imaging Center, University of Southern California 3 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- University of Southern California 5 Molecular and Computational Biology , , 1002 West Childs Way, Los Angeles, CA 90089 , USA
| | - Scott E. Fraser
- Translational Imaging Center, University of Southern California 3 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- Biomedical Engineering, University of Southern California 4 , 1002 West Childs Way, Los Angeles, CA 90089 , USA
- University of Southern California 5 Molecular and Computational Biology , , 1002 West Childs Way, Los Angeles, CA 90089 , USA
| | - Stephan C. F. Neuhauss
- University of Zurich 2 , Department of Molecular and Life Sciences, Winterthurerstrasse 190, 8057 Zürich , Switzerland
| | - Elke A. Ober
- University of Copenhagen, NNF Center for Stem Cell Biology (DanStem) 1 , Blegdamsvej 3B, 2200 Copenhagen N , Denmark
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Okamura K, Yoshino H, Ogawa Y, Yamamuro K, Kimoto S, Yamaguchi Y, Nishihata Y, Ikehara M, Makinodan M, Saito Y, Kishimoto T. Juvenile social isolation immediately affects the synaptic activity and firing property of fast-spiking parvalbumin-expressing interneuron subtype in mouse medial prefrontal cortex. Cereb Cortex 2022; 33:3591-3606. [PMID: 35945688 DOI: 10.1093/cercor/bhac294] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
A lack of juvenile social experience causes various behavioral impairments and brain dysfunction, especially in the medial prefrontal cortex (mPFC). Our previous studies revealed that juvenile social isolation for 2 weeks immediately after weaning affects the synaptic inputs and intrinsic excitability of fast-spiking parvalbumin-expressing (FSPV) interneurons as well as a specific type of layer 5 (L5) pyramidal cells, which we termed prominent h-current (PH) cells, in the mPFC. However, since these changes were observed at the adult age of postnatal day 65 (P65), the primary cause of these changes to neurons immediately after juvenile social isolation (postnatal day 35) remains unknown. Here, we investigated the immediate effects of juvenile social isolation on the excitability and synaptic inputs of PH pyramidal cells and FSPV interneurons at P35 using whole-cell patch-clamp recording. We observed that excitatory inputs to FSPV interneurons increased immediately after juvenile social isolation. We also found that juvenile social isolation increases the firing reactivity of a subtype of FSPV interneurons, whereas only a fractional effect was detected in PH pyramidal cells. These findings suggest that juvenile social isolation primarily disturbs the developmental rebuilding of circuits involving FSPV interneurons and eventually affects the circuits involving PH pyramidal cells in adulthood.
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Affiliation(s)
- Kazuya Okamura
- Department of Psychiatry, Nara Medical University, Kashihara, Nara 634-8522, Japan
| | - Hiroki Yoshino
- Department of Psychiatry, Nara Medical University, Kashihara, Nara 634-8522, Japan.,Mie Prefectural Mental Medical Center, Tsu, Mie 514-0818, Japan
| | - Yoichi Ogawa
- Department of Neurophysiology, Nara Medical University, Kashihara, Nara 634-8522, Japan
| | - Kazuhiko Yamamuro
- Department of Psychiatry, Nara Medical University, Kashihara, Nara 634-8522, Japan
| | - Sohei Kimoto
- Department of Psychiatry, Nara Medical University, Kashihara, Nara 634-8522, Japan.,Department of Neuropsychiatry, Wakayama Medical University, Kimiidera, Wakayama 641-8509, Japan
| | - Yasunari Yamaguchi
- Department of Psychiatry, Nara Medical University, Kashihara, Nara 634-8522, Japan.,Department of Neuropsychiatry, Wakayama Medical University, Kimiidera, Wakayama 641-8509, Japan
| | - Yosuke Nishihata
- Department of Psychiatry, Nara Medical University, Kashihara, Nara 634-8522, Japan
| | - Minobu Ikehara
- Department of Psychiatry, Nara Medical University, Kashihara, Nara 634-8522, Japan
| | - Manabu Makinodan
- Department of Psychiatry, Nara Medical University, Kashihara, Nara 634-8522, Japan
| | - Yasuhiko Saito
- Department of Neurophysiology, Nara Medical University, Kashihara, Nara 634-8522, Japan
| | - Toshifumi Kishimoto
- Department of Psychiatry, Nara Medical University, Kashihara, Nara 634-8522, Japan
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Liu W, Padhi A, Zhang X, Narendran J, Anastasio MA, Nain AS, Irudayaraj J. Dynamic Heterochromatin States in Anisotropic Nuclei of Cells on Aligned Nanofibers. ACS NANO 2022; 16:10754-10767. [PMID: 35803582 PMCID: PMC9332347 DOI: 10.1021/acsnano.2c02660] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The cancer cell nucleus deforms as it invades the interstitial spaces in tissues and the tumor microenvironment. While alteration of the chromatin structure in a deformed nucleus is expected and documented, the chromatin structure in the nuclei of cells on aligned matrices has not been elucidated. In this work we elucidate the spatiotemporal organization of heterochromatin in the elongated nuclei of cells on aligned nanofibers with stimulated emission depletion nanoscopy and fluorescence correlation spectroscopy. We show that the anisotropy of nuclei is sufficient to drive H3K9me3-heterochromatin alterations, with enhanced H3K9me3 nanocluster compaction and aggregation states that otherwise are indistinguishable from diffraction-limited microscopy. We interrogated the higher-order heterochromatin structures within major chromatin compartments in anisotropic nuclei and discovered a wider spatial dispersion of nanodomain clusters in the nucleoplasm and condensed larger nanoclusters near the periphery and pericentromeric heterochromatin. Upon examining the spatiotemporal dynamics of heterochromatin in anisotropic nuclei, we observed reduced mobility of the constitutive heterochromatin mark H3K9me3 and the associated heterochromatin protein 1 (HP1α) at the nucleoplasm and periphery regions, correlating with increased viscosity and changes in gene expression. Since heterochromatin remodeling is crucial to genome integrity, our results reveal an unconventional H3K9me3 heterochromatin distribution, providing cues to an altered chromatin state due to perturbations of the nuclei in aligned fiber configurations.
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Affiliation(s)
- Wenjie Liu
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Cancer Center at Illinois,
Micro and Nanotechnology Laboratory, Beckman
Institute, Carl Woese Institute for Genomic Biology, Urbana, Illinois 61801, United States
| | - Abinash Padhi
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Xiaohui Zhang
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
| | - Jairaj Narendran
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
| | - Mark A. Anastasio
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
| | - Amrinder S. Nain
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Joseph Irudayaraj
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Cancer Center at Illinois,
Micro and Nanotechnology Laboratory, Beckman
Institute, Carl Woese Institute for Genomic Biology, Urbana, Illinois 61801, United States
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29
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Bian WJ, Atrooz F, Patel S, Rababa'h AM. Editorial: Sleep Deprivation, Circadian Misalignment and Addiction Vulnerability in Adolescents. Front Neurosci 2022; 16:940039. [PMID: 35873819 PMCID: PMC9296837 DOI: 10.3389/fnins.2022.940039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wen-Jie Bian
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, United States
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, United States
- *Correspondence: Wen-Jie Bian
| | - Fatin Atrooz
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, United States
| | - Sanket Patel
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, United States
| | - Abeer M. Rababa'h
- Department of Clinical Pharmacy, College of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
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30
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Dyer L, Parker A, Paphiti K, Sanderson J. Lightsheet Microscopy. Curr Protoc 2022; 2:e448. [PMID: 35838628 DOI: 10.1002/cpz1.448] [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: 11/09/2022]
Abstract
In this paper, we review lightsheet (selective plane illumination) microscopy for mouse developmental biologists. There are different means of forming the illumination sheet, and we discuss these. We explain how we introduced the lightsheet microscope economically into our core facility and present our results on fixed and living samples. We also describe methods of clearing fixed samples for three-dimensional imaging and discuss the various means of preparing samples with particular reference to mouse cilia, adipose spheroids, and cochleae. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Laura Dyer
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Andrew Parker
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Keanu Paphiti
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
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31
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Hériché M, Arnould C, Wipf D, Courty PE. Imaging plant tissues: advances and promising clearing practices. TRENDS IN PLANT SCIENCE 2022; 27:601-615. [PMID: 35339361 DOI: 10.1016/j.tplants.2021.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The study of the organ structure of plants and understanding their physiological complexity requires 3D imaging with subcellular resolution. Most plant organs are highly opaque to light, and their study under optical sectioning microscopes is therefore difficult. In animals, many protocols have been developed to make organs transparent to light using clearing protocols (CPs). By contrast, clearing plant tissues is challenging because of the presence of fibers and pigments. We describe progress in the development of plant CPs over the past 20 years through a modified taxonomy of CPs based on their physical and optical parameters that affect tissue properties. We also discuss successful approaches that combine CPs with new microscopy methods and their future applications in plant science research.
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Affiliation(s)
- Mathilde Hériché
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Christine Arnould
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France.
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32
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Swanson JL, Chin PS, Romero JM, Srivastava S, Ortiz-Guzman J, Hunt PJ, Arenkiel BR. Advancements in the Quest to Map, Monitor, and Manipulate Neural Circuitry. Front Neural Circuits 2022; 16:886302. [PMID: 35719420 PMCID: PMC9204427 DOI: 10.3389/fncir.2022.886302] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/27/2022] [Indexed: 01/27/2023] Open
Abstract
Neural circuits and the cells that comprise them represent the functional units of the brain. Circuits relay and process sensory information, maintain homeostasis, drive behaviors, and facilitate cognitive functions such as learning and memory. Creating a functionally-precise map of the mammalian brain requires anatomically tracing neural circuits, monitoring their activity patterns, and manipulating their activity to infer function. Advancements in cell-type-specific genetic tools allow interrogation of neural circuits with increased precision. This review provides a broad overview of recombination-based and activity-driven genetic targeting approaches, contemporary viral tracing strategies, electrophysiological recording methods, newly developed calcium, and voltage indicators, and neurotransmitter/neuropeptide biosensors currently being used to investigate circuit architecture and function. Finally, it discusses methods for acute or chronic manipulation of neural activity, including genetically-targeted cellular ablation, optogenetics, chemogenetics, and over-expression of ion channels. With this ever-evolving genetic toolbox, scientists are continuing to probe neural circuits with increasing resolution, elucidating the structure and function of the incredibly complex mammalian brain.
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Affiliation(s)
- Jessica L. Swanson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Pey-Shyuan Chin
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Juan M. Romero
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
| | - Snigdha Srivastava
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
| | - Joshua Ortiz-Guzman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Patrick J. Hunt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
| | - Benjamin R. Arenkiel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
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33
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Optimized single-step optical clearing solution for 3D volume imaging of biological structures. Commun Biol 2022; 5:431. [PMID: 35534680 PMCID: PMC9085829 DOI: 10.1038/s42003-022-03388-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/21/2022] [Indexed: 12/17/2022] Open
Abstract
Various optical clearing approaches have been introduced to meet the growing demand for 3D volume imaging of biological structures. Each has its own strengths but still suffers from low transparency, long incubation time, processing complexity, tissue deformation, or fluorescence quenching, and a single solution that best satisfies all aspects has yet been developed. Here, we develop OptiMuS, an optimized single-step solution that overcomes the shortcomings of the existing aqueous-based clearing methods and that provides the best performance in terms of transparency, clearing rate, and size retention. OptiMuS achieves rapid and high transparency of brain tissues and other intact organs while preserving the size and fluorescent signal of the tissues. Moreover, OptiMuS is compatible with the use of lipophilic dyes, revealing DiI-labeled vascular structures of the whole brain, kidney, spleen, and intestine, and is also applied to 3D quantitative and comparative analysis of DiI-labeled vascular structures of glomeruli turfs in normal and diseased kidneys. Together, OptiMuS provides a single-step solution for simple, fast, and versatile optical clearing method to obtain high tissue transparency with minimum structural changes and is widely applicable for 3D imaging of various whole biological structures. OptiMuS is an optical clearing method which preserves endogenous fluorescence and sample sizes and can be used to clear thick tissues, visualize neural networks and vascular structures and diagnose pathological status of kidneys, as a potential application.
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34
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A novel renal perivascular mesenchymal cell subset gives rise to fibroblasts distinct from classic myofibroblasts. Sci Rep 2022; 12:5389. [PMID: 35354870 PMCID: PMC8967907 DOI: 10.1038/s41598-022-09331-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Perivascular mesenchymal cells (PMCs), which include pericytes, give rise to myofibroblasts that contribute to chronic kidney disease progression. Several PMC markers have been identified; however, PMC heterogeneity and functions are not fully understood. Here, we describe a novel subset of renal PMCs that express Meflin, a glycosylphosphatidylinositol-anchored protein that was recently identified as a marker of fibroblasts essential for cardiac tissue repair. Tracing the lineage of Meflin+ PMCs, which are found in perivascular and periglomerular areas and exhibit renin-producing potential, showed that they detach from the vasculature and proliferate under disease conditions. Although the contribution of Meflin+ PMCs to conventional α-SMA+ myofibroblasts is low, they give rise to fibroblasts with heterogeneous α-SMA expression patterns. Genetic ablation of Meflin+ PMCs in a renal fibrosis mouse model revealed their essential role in collagen production. Consistent with this, human biopsy samples showed that progressive renal diseases exhibit high Meflin expression. Furthermore, Meflin overexpression in kidney fibroblasts promoted bone morphogenetic protein 7 signals and suppressed myofibroblastic differentiation, implicating the roles of Meflin in suppressing tissue fibrosis. These findings demonstrate that Meflin marks a PMC subset that is functionally distinct from classic pericytes and myofibroblasts, highlighting the importance of elucidating PMC heterogeneity.
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35
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Shan QH, Qin XY, Zhou N, Huang C, Wang Y, Chen P, Zhou JN. A method for ultrafast tissue clearing that preserves fluorescence for multimodal and longitudinal brain imaging. BMC Biol 2022; 20:77. [PMID: 35351101 PMCID: PMC8966190 DOI: 10.1186/s12915-022-01275-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 03/09/2022] [Indexed: 11/25/2022] Open
Abstract
Background Tissue-clearing techniques have recently been developed to make tissues transparent for three-dimensional (3D) imaging at different scales, including single-cell resolution. However, current tissue-clearing workflows have several disadvantages, including complex protocols, time-consuming application, and fluorescence quenching. Additionally, they can be used mainly for clearing larger-volume samples, preventing wide and easy applicability in conventional experimental approaches. In this study, we aimed to develop a versatile, fast, and convenient method for clearing thin and semi-thick samples, which can be used for three-dimensional imaging of experimental or even clinical samples. Results We developed an alkaline solution (AKS) containing a combination of 2,2′-thiodiethanol (TDE), DMSO, D-sorbitol, and Tris for tissue clearing, as the alkaline environment is suitable for maintaining the fluorescence of most commonly used fluorescence protein GFP and its variants, and tested its clearing effect on samples from mice and human brains. We assessed the clearing speed, the preservation of fluorescence protein and dyes, and the imaging depth and quality. The results showed that AKS treatment rapidly cleared 300-μm-thick brain slices and 1-mm-thick slices from different organs within 5 min and 1 h, respectively. Moreover, AKS was compatible with a variety of fluorescence proteins and dyes. Most importantly, AKS enhanced the fluorescence of YFP, in contrast to the majority of existing tissue-clearing methods which reduce the fluorescence intensity of fluorescent proteins. Using AKS, we performed long-time high-resolution imaging of weak fluorescent protein-labelled tissues, long-distance fibre tracking, larger-scale 3D imaging and cell counting of the entire brain area, neural circuit tracing, 3D neuromorphic reconstruction, and 3D histopathology imaging. Conclusions AKS can be used for simple and rapid clearing of samples from mice and human brains and is widely compatible with a variety of fluorescent dyes. Therefore, AKS has great potential to be used as a broad tissue-clearing reagent for biological optical imaging, especially for time-sensitive experiments. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01275-6.
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Affiliation(s)
- Qing-Hong Shan
- Chinese Academy of Science Key Laboratory of Brain Function and Diseases, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Xin-Ya Qin
- Chinese Academy of Science Key Laboratory of Brain Function and Diseases, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Nan Zhou
- Department of Neurosurgery, Huashan Hospital, Fudan University, Middle Urumqi Road 12, Shanghai, 200040, China
| | - Chuan Huang
- Chinese Academy of Science Key Laboratory of Brain Function and Diseases, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Yu Wang
- Chinese Academy of Science Key Laboratory of Brain Function and Diseases, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Peng Chen
- Chinese Academy of Science Key Laboratory of Brain Function and Diseases, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Jiang-Ning Zhou
- Chinese Academy of Science Key Laboratory of Brain Function and Diseases, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China. .,Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
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Brodin ATS, Gabulya S, Wellfelt K, Karlsson TE. Five Hours Total Sleep Deprivation Does Not Affect CA1 Dendritic Length or Spine Density. Front Synaptic Neurosci 2022; 14:854160. [PMID: 35359703 PMCID: PMC8964138 DOI: 10.3389/fnsyn.2022.854160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Sleep is essential for long term memory function. However, the neuroanatomical consequences of sleep loss are disputed. Sleep deprivation has been reported to cause both decreases and increases of dendritic spine density. Here we use Thy1-GFP expressing transgenic mice to investigate the effects of acute sleep deprivation on the dendritic architecture of hippocampal CA1 pyramidal neurons. We found that 5 h of sleep deprivation had no effect on either dendritic length or dendritic spine density. Our work suggests that no major neuroanatomical changes result from a single episode of sleep deprivation.
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Affiliation(s)
| | - Sarolta Gabulya
- Institute of Neuroinformatics, University of Zurich and ETH, Zürich, Switzerland
| | - Katrin Wellfelt
- Department of Neuroscience, Karolinska Institutet, Solna, Sweden
| | - Tobias E. Karlsson
- Department of Neuroscience, Karolinska Institutet, Solna, Sweden
- *Correspondence: Tobias E. Karlsson,
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37
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Probing Dynamic Variation of Layered Microstructure Using Backscattering Polarization Imaging. PHOTONICS 2022. [DOI: 10.3390/photonics9030153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Polarization imaging can quantitatively probe the microscopic structure of biological tissues which can be complex and consist of layered structures. In this paper, we established a fast-backscattering Mueller matrix imaging system to characterize the dynamic variation in the microstructure of single-layer and double-layer tissues as glycerin solution penetrated into the samples. The characteristic response of Mueller matrix elements, as well as polarization parameters with clearer physics meanings, show that polarization imaging can capture the dynamic variation in the layered microstructure. The experimental results are confirmed by Monte Carlo simulations. Further examination on the accuracy of Mueller matrix measurements also shows that much faster speed has to be considered when backscattering Mueller matrix imaging is applied to living samples.
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38
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Carabaña C, Lloyd-Lewis B. Multidimensional Fluorescence Imaging of Embryonic and Postnatal Mammary Gland Development. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2471:19-48. [PMID: 35175590 DOI: 10.1007/978-1-0716-2193-6_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Multidimensional fluorescence imaging represents a powerful approach for studying the dynamic cellular processes underpinning the development, function, and maintenance of the mammary gland. Here, we describe key multidimensional imaging strategies that enable visualization of mammary branching morphogenesis and epithelial cell fate dynamics during postnatal and embryonic mammary gland development. These include 4-dimensional intravital microscopy and ex vivo imaging of embryonic mammary cultures, in addition to methods that facilitate 3-dimensional imaging of the ductal epithelium at single-cell resolution within its native stroma. Collectively, these approaches provide a window into mammary developmental dynamics, and the perturbations underlying tissue dysfunction and disease.
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Affiliation(s)
- Claudia Carabaña
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France.,Sorbonne University, UPMC University of Paris VI, Paris, France
| | - Bethan Lloyd-Lewis
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
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39
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Multicolor strategies for investigating clonal expansion and tissue plasticity. Cell Mol Life Sci 2022; 79:141. [PMID: 35187598 PMCID: PMC8858928 DOI: 10.1007/s00018-021-04077-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/27/2021] [Accepted: 10/14/2021] [Indexed: 12/20/2022]
Abstract
Understanding the generation of complexity in living organisms requires the use of lineage tracing tools at a multicellular scale. In this review, we describe the different multicolor strategies focusing on mouse models expressing several fluorescent reporter proteins, generated by classical (MADM, Brainbow and its multiple derivatives) or acute (StarTrack, CLoNe, MAGIC Markers, iOn, viral vectors) transgenesis. After detailing the multi-reporter genetic strategies that serve as a basis for the establishment of these multicolor mouse models, we briefly mention other animal and cellular models (zebrafish, chicken, drosophila, iPSC) that also rely on these constructs. Then, we highlight practical applications of multicolor mouse models to better understand organogenesis at single progenitor scale (clonal analyses) in the brain and briefly in several other tissues (intestine, skin, vascular, hematopoietic and immune systems). In addition, we detail the critical contribution of multicolor fate mapping strategies in apprehending the fine cellular choreography underlying tissue morphogenesis in several models with a particular focus on brain cytoarchitecture in health and diseases. Finally, we present the latest technological advances in multichannel and in-depth imaging, and automated analyses that enable to better exploit the large amount of data generated from multicolored tissues.
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40
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Woo J, Lee EY, Lee M, Ku S, Park JY, Cho YE. Comparative Analyses of Clearing Efficacies of Tissue Clearing Protocols by Using a Punching Assisted Clarity Analysis. Front Bioeng Biotechnol 2022; 9:784626. [PMID: 35155401 PMCID: PMC8831720 DOI: 10.3389/fbioe.2021.784626] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/30/2021] [Indexed: 02/03/2023] Open
Abstract
The advent of tissue clearing methods, in conjunction with novel high-resolution imaging techniques, has enabled the visualization of three-dimensional structures with unprecedented depth and detail. Although a variety of clearing protocols have been developed, little has been done to quantify their efficacies in a systematic, reproducible fashion. Here, we present two simple assays, Punching-Assisted Clarity Analysis (PACA)-Light and PACA-Glow, which use easily accessible spectroscopy and gel documentation systems to quantify the transparency of multiple cleared tissues simultaneously. We demonstrate the use of PACA-Light and PACA-Glow to compare twenty-eight tissue clearing protocols on rodent brains. We also show that regional differences exist in tissue transparency in the rodent brain, with cerebellar tissue consistently achieving lower clearing levels compared to the prefrontal or cerebral cortex across all protocols. This represents the largest comparative study of tissue clearing protocols to date, made possible by the high-throughput nature of our PACA platforms.
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Affiliation(s)
- Jiwon Woo
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Institute, Biohedron Therapeutics Co., Ltd., Seoul, South Korea
| | - Eunice Yoojin Lee
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Mirae Lee
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Seockmo Ku
- Fermentation Science Program, School of Agriculture, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Jeong-Yoon Park
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Yong Eun Cho
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
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41
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Sakamoto Y, Ishimoto A, Sakai Y, Sato M, Nishihama R, Abe K, Sano Y, Furuichi T, Tsuji H, Kohchi T, Matsunaga S. Improved clearing method contributes to deep imaging of plant organs. Commun Biol 2022; 5:12. [PMID: 35013509 PMCID: PMC8748589 DOI: 10.1038/s42003-021-02955-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 12/08/2021] [Indexed: 01/01/2023] Open
Abstract
Tissue clearing methods are increasingly essential for the microscopic observation of internal tissues of thick biological organs. We previously developed TOMEI, a clearing method for plant tissues; however, it could not entirely remove chlorophylls nor reduce the fluorescent signal of fluorescent proteins. Here, we developed an improved TOMEI method (iTOMEI) to overcome these limitations. First, a caprylyl sulfobetaine was determined to efficiently remove chlorophylls from Arabidopsis thaliana seedlings without GFP quenching. Next, a weak alkaline solution restored GFP fluorescence, which was mainly lost during fixation, and an iohexol solution with a high refractive index increased sample transparency. These procedures were integrated to form iTOMEI. iTOMEI enables the detection of much brighter fluorescence than previous methods in tissues of A. thaliana, Oryza sativa, and Marchantia polymorpha. Moreover, a mouse brain was also efficiently cleared by the iTOMEI-Brain method within 48 h, and strong fluorescent signals were detected in the cleared brain. Sakamoto et al. demonstrate an improved optical clearing method, iTOMEI, for plant imaging. The new method can achieve fast clearing and effective removal of autofluorescence signals, and at the same time preserve signals from desired fluorescence proteins.
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Affiliation(s)
- Yuki Sakamoto
- Imaging Frontier Center, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.,Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama-cho 1-1, Toyonaka, Osaka, 560-0043, Japan
| | - Anna Ishimoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Yuuki Sakai
- Department of Biology, Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Moeko Sato
- Kihara Institute for Biological Research, Yokohama City University, Maioka 641-12, Totsuka, Yokohama, 244-0813, Japan
| | - Ryuichi Nishihama
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.,Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Konami Abe
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Yoshitake Sano
- Imaging Frontier Center, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.,Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Teiichi Furuichi
- Imaging Frontier Center, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.,Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Maioka 641-12, Totsuka, Yokohama, 244-0813, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Sachihiro Matsunaga
- Imaging Frontier Center, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan. .,Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan. .,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
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42
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Liu L, Xia X, Xiang F, Gao Y, Li X, Li H, Zheng W. F-CUBIC: a rapid optical clearing method optimized by quantitative evaluation. BIOMEDICAL OPTICS EXPRESS 2022; 13:237-251. [PMID: 35154867 PMCID: PMC8803013 DOI: 10.1364/boe.442976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
In recent decades, various powerful optical clearing methods have emerged to facilitate deep-tissue imaging. However, a rapid and safe protocol for millimeter-thick specimens is still desired. In this study, we propose a simple and economical chemical screening method that uses porcine small intestine tissue as the testing sample to quantify the clearing speed of different optical clearing reagents. By screening with this method, we developed a fast and versatile clearing protocol, termed F-CUBIC (adding formamide to CUBIC). F-CUBIC allows easy clearing of millimeter-thick tissues within 2-20 min by one-step immersion at room temperature. It introduces negligible tissue distortion and shows high compatibility with various fluorescent labeling techniques. Based on endoscopic human colon specimens, we successfully demonstrated the potential of F-CUBIC for nondestructive three-dimensional (3D) biopsy in combination with two-photon microscopy. This study would substantially benefit rapid 3D tissue mapping in biomedical research and clinics, such as instant histopathological examinations.
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Affiliation(s)
- Lina Liu
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Authors contributed equally to this work
| | - Xianyuan Xia
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Authors contributed equally to this work
| | - Feng Xiang
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yufeng Gao
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xi Li
- Department of Gastroenterology, Peking University Shenzhen Hospital, Shen Zhen 518036, China
| | - Hui Li
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wei Zheng
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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43
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Pende M, Saghafi S, Becker K, Hummel T, Dodt HU. FlyClear: A Tissue-Clearing Technique for High-Resolution Microscopy of Drosophila. Methods Mol Biol 2022; 2540:349-359. [PMID: 35980588 DOI: 10.1007/978-1-0716-2541-5_18] [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: 06/15/2023]
Abstract
Fluorescently labeled transgenic lines of Drosophila melanogaster are a powerful routine tool in fly laboratories. The possibility to fluorescently visualize individual cell populations or entire tissues and the constantly improving microscopy technologies such as two-photon or light-sheet applications, with deep tissue imaging, hold great potential to address central biological questions at an organismic level. However, strong pigmentation and the opaque nature of the D. melanogaster cuticle hinder the penetration of visible light into internal tissues, thereby limiting the application of fluorescent microscopes to analyses of the outermost surfaces of intact samples. In addition, tissue-induced light scattering and optical aberrations quickly blur the view and, hence, require tissue sectioning for further investigation. We have developed a tissue-clearing and depigmentation approach (FlyClear), which preserves endogenous fluorescent signals and is applicable to various developmental stages ranging from larvae to adult fruit flies (Pende et al. Nature communications 9:4731, 2018). In this chapter, we provide a detailed protocol of the experimental steps involved.
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Affiliation(s)
- Marko Pende
- Mount Desert Island Biological Laboratory (MDIBL), Salisbury, USA.
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
| | - Saiedeh Saghafi
- Department for Bioelectronics, FKE, Vienna University of Technology, Vienna, Austria
| | - Klaus Becker
- Department for Bioelectronics, FKE, Vienna University of Technology, Vienna, Austria
| | - Thomas Hummel
- Department of Neurobiology, University of Vienna, Vienna, Austria
| | - Hans-Ulrich Dodt
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
- Department for Bioelectronics, FKE, Vienna University of Technology, Vienna, Austria.
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44
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Na M, Kim K, Oh K, Choi HJ, Ha C, Chang S. Sodium Cholate-Based Active Delipidation for Rapid and Efficient Clearing and Immunostaining of Deep Biological Samples. SMALL METHODS 2022; 6:e2100943. [PMID: 35041279 DOI: 10.1002/smtd.202100943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/29/2021] [Indexed: 06/14/2023]
Abstract
Recent surges of optical clearing provided anatomical maps to understand structure-function relationships at organ scale. Detergent-mediated lipid removal enhances optical clearing and allows efficient penetration of antibodies inside tissues, and sodium dodecyl sulfate (SDS) is the most common choice for this purpose. SDS, however, forms large micelles and has a low critical micelle concentration (CMC). Theoretically, detergents that form smaller micelles and higher CMC should perform better but these have remained mostly unexplored. Here, SCARF, a sodium cholate (SC)-based active delipidation method, is developed for better clearing and immunolabeling of thick tissues or whole organs. It is found that SC has superior properties to SDS as a detergent but has serious problems; precipitation and browning. These limitations are overcome by using the ion-conductive film to confine SC while enabling high conductivity. SCARF renders orders of magnitude faster tissue transparency than the SDS-based method, while excellently preserving the endogenous fluorescence, and enables much efficient penetration of a range of antibodies, thus revealing structural details of various organs including sturdy post-mortem human brain tissues at the cellular resolution. Thus, SCARF represents a robust and superior alternative to the SDS-based clearing methods and is expected to facilitate the 3D morphological mapping of various organs.
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Affiliation(s)
- Myeongsu Na
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Kitae Kim
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Kyoungjoon Oh
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Hyung Jin Choi
- Department of Anatomy and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - ChangMan Ha
- Research Division and Brain Research Core Facility, Korea Brain Research Institute, Daegu, 41068, South Korea
| | - Sunghoe Chang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, 03080, South Korea
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45
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Leiwe MN, Fujimoto S, Imai T. Post hoc Correction of Chromatic Aberrations in Large-Scale Volumetric Images in Confocal Microscopy. Front Neuroanat 2021; 15:760063. [PMID: 34955764 PMCID: PMC8703134 DOI: 10.3389/fnana.2021.760063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/12/2021] [Indexed: 12/03/2022] Open
Abstract
Over the last decade, tissue-clearing techniques have expanded the scale of volumetric fluorescence imaging of the brain, allowing for the comprehensive analysis of neuronal circuits at a millimeter scale. Multicolor imaging is particularly powerful for circuit tracing with fluorescence microscopy. However, multicolor imaging of large samples often suffers from chromatic aberration, where different excitation wavelengths of light have different focal points. In this study, we evaluated chromatic aberrations for representative objective lenses and a clearing agent with confocal microscopy and found that axial aberration is particularly problematic. Moreover, the axial chromatic aberrations were often depth-dependent. Therefore, we developed a program that is able to align depths for different fluorescence channels based on reference samples with fluorescent beads or data from guide stars within biological samples. We showed that this correction program can successfully correct chromatic aberrations found in confocal images of multicolor-labeled brain tissues. Our simple post hoc correction strategy is useful to obtain large-scale multicolor images of cleared tissues with minimal chromatic aberrations.
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Affiliation(s)
- Marcus N Leiwe
- Department of Developmental Neurophysiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Satoshi Fujimoto
- Department of Developmental Neurophysiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Imai
- Department of Developmental Neurophysiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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46
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Endo M, Maruoka H, Okabe S. Advanced Technologies for Local Neural Circuits in the Cerebral Cortex. Front Neuroanat 2021; 15:757499. [PMID: 34803616 PMCID: PMC8595196 DOI: 10.3389/fnana.2021.757499] [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: 08/12/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
The neural network in the brain can be viewed as an integrated system assembled from a large number of local neural circuits specialized for particular brain functions. Activities of neurons in local neural circuits are thought to be organized both spatially and temporally under the rules optimized for their roles in information processing. It is well perceived that different areas of the mammalian neocortex have specific cognitive functions and distinct computational properties. However, the organizational principles of the local neural circuits in different cortical regions have not yet been clarified. Therefore, new research principles and related neuro-technologies that enable efficient and precise recording of large-scale neuronal activities and synaptic connections are necessary. Innovative technologies for structural analysis, including tissue clearing and expansion microscopy, have enabled super resolution imaging of the neural circuits containing thousands of neurons at a single synapse resolution. The imaging resolution and volume achieved by new technologies are beyond the limits of conventional light or electron microscopic methods. Progress in genome editing and related technologies has made it possible to label and manipulate specific cell types and discriminate activities of multiple cell types. These technologies will provide a breakthrough for multiscale analysis of the structure and function of local neural circuits. This review summarizes the basic concepts and practical applications of the emerging technologies and new insight into local neural circuits obtained by these technologies.
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Affiliation(s)
| | | | - Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
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47
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Almagro J, Messal HA, Zaw Thin M, van Rheenen J, Behrens A. Tissue clearing to examine tumour complexity in three dimensions. Nat Rev Cancer 2021; 21:718-730. [PMID: 34331034 DOI: 10.1038/s41568-021-00382-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/18/2021] [Indexed: 02/07/2023]
Abstract
The visualization of whole organs and organisms through tissue clearing and fluorescence volumetric imaging has revolutionized the way we look at biological samples. Its application to solid tumours is changing our perception of tumour architecture, revealing signalling networks and cell interactions critical in tumour progression, and provides a powerful new strategy for cancer diagnostics. This Review introduces the latest advances in tissue clearing and three-dimensional imaging, examines the challenges in clearing epithelia - the tissue of origin of most malignancies - and discusses the insights that tissue clearing has brought to cancer research, as well as the prospective applications to experimental and clinical oncology.
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Affiliation(s)
- Jorge Almagro
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | - Hendrik A Messal
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - May Zaw Thin
- Cancer Stem Cell Laboratory, Institute of Cancer Research, London, UK
| | - Jacco van Rheenen
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Axel Behrens
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK.
- Cancer Stem Cell Laboratory, Institute of Cancer Research, London, UK.
- Convergence Science Centre and Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK.
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48
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Zhu J, Liu X, Deng Y, Li D, Yu T, Zhu D. Tissue optical clearing for 3D visualization of vascular networks: A review. Vascul Pharmacol 2021; 141:106905. [PMID: 34506969 DOI: 10.1016/j.vph.2021.106905] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/01/2022]
Abstract
Reconstruction of the vasculature of intact tissues/organs down to the capillary level is essential for understanding the development and remodeling of vascular networks under physiological and pathological conditions. Optical imaging techniques can provide sufficient resolution to distinguish small vessels with several microns, but the imaging depth is somewhat limited due to the high light scattering of opaque tissue. Recently, various tissue optical clearing methods have been developed to overcome light attenuation and improve the imaging depth both for ex-vivo and in-vivo visualizations. Tissue clearing combined with vessel labeling techniques and advanced optical tomography enables successful mapping of the vasculature of different tissues/organs, as well as dynamically monitoring vessel function under normal and pathological conditions. Here, we briefly introduce the commonly-used labeling strategies for entire vascular networks, the current tissue optical clearing techniques available for various tissues, as well as the advanced optical imaging techniques for fast, high-resolution structural and functional imaging for blood vessels. We also discuss the applications of these techniques in the 3D visualization of vascular networks in normal tissues, and the vascular remodeling in several typical pathological models in clinical research. This review is expected to provide valuable insights for researchers to study the potential mechanisms of various vessel-associated diseases using tissue optical clearing pipeline.
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Affiliation(s)
- Jingtan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaomei Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yating Deng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dongyu Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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49
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Abstract
Tissue clearing increases the transparency of late developmental stages and enables deep imaging in fixed organisms. Successful implementation of these methodologies requires a good grasp of sample processing, imaging and the possibilities offered by image analysis. In this Primer, we highlight how tissue clearing can revolutionize the histological analysis of developmental processes and we advise on how to implement effective clearing protocols, imaging strategies and analysis methods for developmental biology.
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Affiliation(s)
| | - Nicolas Renier
- Sorbonne Université, Paris Brain Institute – ICM, INSERM, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
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50
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Zhu J, Ma Y, Xu J, Li Y, Wan P, Qi Y, Yu T, Zhu D. Dec-DISCO: decolorization DISCO clearing for seeing through the biological architectures of heme-rich organs. BIOMEDICAL OPTICS EXPRESS 2021; 12:5499-5513. [PMID: 34692197 PMCID: PMC8515970 DOI: 10.1364/boe.431397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/11/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
The tissue optical clearing technique plays an important role in three-dimensional (3D) visualization of large tissues. As a typical solvent-based clearing method, 3DISCO can achieve the highest level of tissue transparency with favorable clearing speed. However, 3DISCO cannot deal with the residual blood within tissues, leading to tissue brownness or redness after clearing, thus greatly influencing the tissue transparency and image quality due to the strong absorption of residual blood. To address this problem, we proposed an optimized clearing method by introducing CUBIC-L solution combined with 3DISCO for effective decolorization, termed Dec-DISCO (Decolorization DISCO). Dec-DISCO achieves better transparency than 3DISCO for various heme-rich tissues and performs enhanced fluorescence preservation capability. Dec-DISCO allows high-quality 3D imaging of fluorescently labeled heme-rich organs, as well as pathological tissue with severe hemorrhage. Dec-DISCO is expected to provide a powerful tool for histological analysis of kinds of heme-rich tissues in various medical conditions.
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Affiliation(s)
- Jingtan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yilin Ma
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jianyi Xu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yusha Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Peng Wan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yisong Qi
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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