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Kim J, Hong J, Park K, Lee S, Hoang AT, Pak S, Zhao H, Ji S, Yang S, Chung CK, Yang S, Ahn JH. Injectable 2D Material-Based Sensor Array for Minimally Invasive Neural Implants. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2400261. [PMID: 38741451 DOI: 10.1002/adma.202400261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/16/2024] [Indexed: 05/16/2024]
Abstract
Intracranial implants for diagnosis and treatment of brain diseases have been developed over the past few decades. However, the platform of conventional implantable devices still relies on invasive probes and bulky sensors in conjunction with large-area craniotomy and provides only limited biometric information. Here, an implantable multi-modal sensor array that can be injected through a small hole in the skull and inherently spread out for conformal contact with the cortical surface is reported. The injectable sensor array, composed of graphene multi-channel electrodes for neural recording and electrical stimulation and MoS2-based sensors for monitoring intracranial temperature and pressure, is designed based on a mesh structure whose elastic restoring force enables the contracted device to spread out. It is demonstrated that the sensor array injected into a rabbit's head can detect epileptic discharges on the surface of the cortex and mitigate it by electrical stimulation while monitoring both intracranial temperature and pressure. This method provides good potential for implanting a variety of functional devices via minimally invasive surgery.
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Affiliation(s)
- Jejung Kim
- School of Electrical and Electronic Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Juyeong Hong
- School of Electrical and Electronic Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Kyungtai Park
- School of Electrical and Electronic Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sangwon Lee
- gBrain Inc., Incheon, 21984, Republic of Korea
| | - Anh Tuan Hoang
- School of Electrical and Electronic Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sojeong Pak
- Department of Neuroscience, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong
| | - Huilin Zhao
- Department of Neuroscience, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong
| | - Seunghyeon Ji
- School of Electrical and Electronic Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sungchil Yang
- Department of Nanobioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Chun Kee Chung
- Department of Neurosurgery, Seoul National University Hospital, Seoul, 03080, Republic of Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Sunggu Yang
- gBrain Inc., Incheon, 21984, Republic of Korea
- Department of Neuroscience, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong
| | - Jong-Hyun Ahn
- School of Electrical and Electronic Engineering, Yonsei University, Seoul, 03722, Republic of Korea
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2
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Mino T, Nonaka H, Hamachi I. Molecular anchoring and fluorescent labeling in animals compatible with tissue clearing for 3D imaging. Curr Opin Chem Biol 2024; 81:102474. [PMID: 38838505 DOI: 10.1016/j.cbpa.2024.102474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024]
Abstract
Analyzing the quantity and distribution of molecules throughout intact biological tissue is crucial for understanding various biological phenomena. Traditional methods involving destructive extraction result in the loss of spatial information. Conversely, tissue-clearing techniques combined with fluorescence imaging have recently emerged as a powerful tool for deep tissue imaging without sacrificing spatial coverage. Key to this approach is the anchoring and labeling of targets in intact tissue. In this review, methods for anchoring and labeling proteins, lipids, carbohydrates, and small molecules are presented. Future directions include the development of activity-based probes that work in vivo and mark transient events with spatial information to enable a deeper understanding of biological phenomena.
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Affiliation(s)
- Takeharu Mino
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hiroshi Nonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan.
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3
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Tamura I, Sakamoto DM, Yi B, Saito Y, Yamada N, Morimoto J, Takakusagi Y, Kuroda M, Kubota SI, Yatabe H, Kobayashi M, Harada H, Tainaka K, Sando S. Click3D: Click reaction across deep tissues for whole-organ 3D fluorescence imaging. SCIENCE ADVANCES 2024; 10:eado8471. [PMID: 39018410 PMCID: PMC466963 DOI: 10.1126/sciadv.ado8471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 06/11/2024] [Indexed: 07/19/2024]
Abstract
Click chemistry offers various applications through efficient bioorthogonal reactions. In bioimaging, pretargeting strategies have often been used, using click reactions between molecular probes with a click handle and reporter molecules that make them observable. Recent efforts have integrated tissue-clearing techniques with fluorescent labeling through click chemistry, allowing high-resolution three-dimensional fluorescence imaging. Nevertheless, these techniques have faced a challenge in limited staining depth, confining their use to imaging tissue sections or partial organs. In this study, we introduce Click3D, a method for thoroughly staining whole organs using click chemistry. We identified click reaction conditions that improve staining depth with our custom-developed assay. The Click3D protocol exhibits a greater staining depth compared to conventional methods. Using Click3D, we have successfully achieved whole-kidney imaging of nascent RNA and whole-tumor imaging of hypoxia. We have also accomplished whole-brain imaging of hypoxia by using the clickable hypoxia probe, which has a small size and, therefore, has high permeability to cross the blood-brain barrier.
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Affiliation(s)
- Iori Tamura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Daichi M. Sakamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Bo Yi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yutaro Saito
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Naoki Yamada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yoichi Takakusagi
- Quantum Hyperpolarized MRI Research Team, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Masafumi Kuroda
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shimpei I. Kubota
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Kita-15, Nishi-7, Kita-ku, Sapporo, Hokkaido 060-0815, Japan
| | - Hiroyuki Yatabe
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Minoru Kobayashi
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Genome Dynamics, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Harada
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Genome Dynamics, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata 951-8585, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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4
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Glaser A, Chandrashekar J, Vasquez S, Arshadi C, Ouellette N, Jiang X, Baka J, Kovacs G, Woodard M, Seshamani S, Cao K, Clack N, Recknagel A, Grim A, Balaram P, Turschak E, Hooper M, Liddell A, Rohde J, Hellevik A, Takasaki K, Erion Barner L, Logsdon M, Chronopoulos C, de Vries S, Ting J, Perlmutter S, Kalmbach B, Dembrow N, Tasic B, Reid RC, Feng D, Svoboda K. Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.08.544277. [PMID: 37425699 PMCID: PMC10327101 DOI: 10.1101/2023.06.08.544277] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Recent advances in tissue processing, labeling, and fluorescence microscopy are providing unprecedented views of the structure of cells and tissues at sub-diffraction resolutions and near single molecule sensitivity, driving discoveries in diverse fields of biology, including neuroscience. Biological tissue is organized over scales of nanometers to centimeters. Harnessing molecular imaging across intact, three-dimensional samples on this scale requires new types of microscopes with larger fields of view and working distance, as well as higher throughput. We present a new expansion-assisted selective plane illumination microscope (ExA-SPIM) with aberration-free 1×1×3 μm optical resolution over a large field of view (10.6×8.0 mm 2 ) and working distance (35 mm) at speeds up to 946 megavoxels/sec. Combined with new tissue clearing and expansion methods, the microscope allows imaging centimeter-scale samples with 250×250×750 nm optical resolution (4× expansion), including entire mouse brains, with high contrast and without sectioning. We illustrate ExA-SPIM by reconstructing individual neurons across the mouse brain, imaging cortico-spinal neurons in the macaque motor cortex, and visualizing axons in human white matter.
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5
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Kon K, Ode KL, Mano T, Fujishima H, Takahashi RR, Tone D, Shimizu C, Shiono S, Yada S, Matsuzawa K, Yoshida SY, Yoshida Garçon J, Kaneko M, Shinohara Y, Yamada RG, Shi S, Miyamichi K, Sumiyama K, Kiyonari H, Susaki EA, Ueda HR. Cortical parvalbumin neurons are responsible for homeostatic sleep rebound through CaMKII activation. Nat Commun 2024; 15:6054. [PMID: 39025867 PMCID: PMC11258272 DOI: 10.1038/s41467-024-50168-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/01/2024] [Indexed: 07/20/2024] Open
Abstract
The homeostatic regulation of sleep is characterized by rebound sleep after prolonged wakefulness, but the molecular and cellular mechanisms underlying this regulation are still unknown. In this study, we show that Ca2+/calmodulin-dependent protein kinase II (CaMKII)-dependent activity control of parvalbumin (PV)-expressing cortical neurons is involved in homeostatic regulation of sleep in male mice. Prolonged wakefulness enhances cortical PV-neuron activity. Chemogenetic suppression or activation of cortical PV neurons inhibits or induces rebound sleep, implying that rebound sleep is dependent on increased activity of cortical PV neurons. Furthermore, we discovered that CaMKII kinase activity boosts the activity of cortical PV neurons, and that kinase activity is important for homeostatic sleep rebound. Here, we propose that CaMKII-dependent PV-neuron activity represents negative feedback inhibition of cortical neural excitability, which serves as the distributive cortical circuits for sleep homeostatic regulation.
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Affiliation(s)
- Kazuhiro Kon
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Kennedy Krieger Institute, Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
| | - Tomoyuki Mano
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Computational Neuroethology Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - Hiroshi Fujishima
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Department of Systems Biology, Institute of Life Science, Kurume University, Kurume, Fukuoka, Japan
| | - Riina R Takahashi
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Daisuke Tone
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
| | - Chika Shimizu
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
| | - Shinnosuke Shiono
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Saori Yada
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kyoko Matsuzawa
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
| | - Shota Y Yoshida
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
| | - Junko Yoshida Garçon
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Izumi, Osaka, Japan
| | - Mari Kaneko
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research (BDR), Chuou-ku, Kobe, Hyogo, Japan
| | - Yuta Shinohara
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Rikuhiro G Yamada
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Department of Systems Biology, Institute of Life Science, Kurume University, Kurume, Fukuoka, Japan
| | - Shoi Shi
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kazunari Miyamichi
- Laboratory for Comparative Connectomics, RIKEN Center for Biosystems Dynamics Research (BDR), Chuou-ku, Kobe, Hyogo, Japan
| | - Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research (BDR), Chuou-ku, Kobe, Hyogo, Japan
| | - Etsuo A Susaki
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan.
- Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Department of Systems Biology, Institute of Life Science, Kurume University, Kurume, Fukuoka, Japan.
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6
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Ding Y, Huang Y, Gao P, Thai A, Chilaparasetti AN, Gopi M, Xu X, Li C. Brain image data processing using collaborative data workflows on Texera. Front Neural Circuits 2024; 18:1398884. [PMID: 39050044 PMCID: PMC11266044 DOI: 10.3389/fncir.2024.1398884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/20/2024] [Indexed: 07/27/2024] Open
Abstract
In the realm of neuroscience, mapping the three-dimensional (3D) neural circuitry and architecture of the brain is important for advancing our understanding of neural circuit organization and function. This study presents a novel pipeline that transforms mouse brain samples into detailed 3D brain models using a collaborative data analytics platform called "Texera." The user-friendly Texera platform allows for effective interdisciplinary collaboration between team members in neuroscience, computer vision, and data processing. Our pipeline utilizes the tile images from a serial two-photon tomography/TissueCyte system, then stitches tile images into brain section images, and constructs 3D whole-brain image datasets. The resulting 3D data supports downstream analyses, including 3D whole-brain registration, atlas-based segmentation, cell counting, and high-resolution volumetric visualization. Using this platform, we implemented specialized optimization methods and obtained significant performance enhancement in workflow operations. We expect the neuroscience community can adopt our approach for large-scale image-based data processing and analysis.
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Affiliation(s)
- Yunyan Ding
- Department of Computer Science, University of California, Irvine, Irvine, CA, United States
| | - Yicong Huang
- Department of Computer Science, University of California, Irvine, Irvine, CA, United States
| | - Pan Gao
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Andy Thai
- Department of Computer Science, University of California, Irvine, Irvine, CA, United States
| | | | - M. Gopi
- Department of Computer Science, University of California, Irvine, Irvine, CA, United States
| | - Xiangmin Xu
- Department of Computer Science, University of California, Irvine, Irvine, CA, United States
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- The Center for Neural Circuit Mapping, University of California, Irvine, Irvine, CA, United States
| | - Chen Li
- Department of Computer Science, University of California, Irvine, Irvine, CA, United States
- The Center for Neural Circuit Mapping, University of California, Irvine, Irvine, CA, United States
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7
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Kaneko Y, Masuda T, Takamatsu K, Mikami S, Nakamura K, Nishihara H, Mizuno R, Tanaka N, Oya M. Volumetric imaging of the tumor microvasculature reflects outcomes and genomic states of clear cell renal cell carcinoma. J Pathol Clin Res 2024; 10:e12388. [PMID: 38923836 PMCID: PMC11200083 DOI: 10.1002/2056-4538.12388] [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: 02/24/2024] [Revised: 04/23/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024]
Abstract
Tumor structure is heterogeneous and complex, and it is difficult to obtain complete characteristics by two-dimensional analysis. The aim of this study was to visualize and characterize volumetric vascular information of clear cell renal cell carcinoma (ccRCC) tumors using whole tissue phenotyping and three-dimensional light-sheet microscopy. Here, we used the diagnosing immunolabeled paraffin-embedded cleared organs pipeline for tissue clearing, immunolabeling, and three-dimensional imaging. The spatial distributions of CD34, which targets blood vessels, and LYVE-1, which targets lymphatic vessels, were examined by calculating three-dimensional density, vessel length, vessel radius, and density curves, such as skewness, kurtosis, and variance of the expression. We then examined those associations with ccRCC outcomes and genetic alteration state. Formalin-fixed paraffin-embedded tumor samples from 46 ccRCC patients were included in the study. Receiver operating characteristic curve analyses revealed the associations between blood vessel and lymphatic vessel distributions and pathological factors such as a high nuclear grade, large tumor size, and the presence of venous invasion. Furthermore, three-dimensional imaging parameters stratified ccRCC patients regarding survival outcomes. An analysis of genomic alterations based on volumetric vascular information parameters revealed that PI3K-mTOR pathway mutations related to the blood vessel radius were significantly different. Collectively, we have shown that the spatial elucidation of volumetric vasculature information could be prognostic and may serve as a new biomarker for genomic alterations. High-end tissue clearing techniques and volumetric immunohistochemistry enable three-dimensional analysis of tumors, leading to a better understanding of the microvascular structure in the tumor space.
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Affiliation(s)
- Yuta Kaneko
- Department of UrologyKeio University School of MedicineTokyoJapan
| | - Tsukasa Masuda
- Department of UrologyKeio University School of MedicineTokyoJapan
| | | | - Shuji Mikami
- Department of Diagnostic PathologyKeio University HospitalTokyoJapan
- Department of Diagnostic PathologyNational Hospital Organization Saitama HospitalSaitamaJapan
| | - Kohei Nakamura
- Genomics Unit, Keio Cancer CenterKeio University School of MedicineTokyoJapan
| | - Hiroshi Nishihara
- Genomics Unit, Keio Cancer CenterKeio University School of MedicineTokyoJapan
| | - Ryuichi Mizuno
- Department of UrologyKeio University School of MedicineTokyoJapan
| | - Nobuyuki Tanaka
- Department of UrologyKeio University School of MedicineTokyoJapan
| | - Mototsugu Oya
- Department of UrologyKeio University School of MedicineTokyoJapan
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8
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Baek S, Jang J, Jung HJ, Lee H, Choe Y. Advanced Immunolabeling Method for Optical Volumetric Imaging Reveals Dystrophic Neurites of Dopaminergic Neurons in Alzheimer's Disease Mouse Brain. Mol Neurobiol 2024; 61:3976-3999. [PMID: 38049707 PMCID: PMC11236860 DOI: 10.1007/s12035-023-03823-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023]
Abstract
Optical brain clearing combined with immunolabeling is valuable for analyzing molecular tissue structures, including complex synaptic connectivity. However, the presence of aberrant lipid deposition due to aging and brain disorders poses a challenge for achieving antibody penetration throughout the entire brain volume. Herein, we present an efficient brain-wide immunolabeling method, the immuno-active clearing technique (iACT). The treatment of brain tissues with a zwitterionic detergent, specifically SB3-12, significantly enhanced tissue permeability by effectively mitigating lipid barriers. Notably, Quadrol treatment further refines the methodology by effectively eliminating residual detergents from cleared brain tissues, subsequently amplifying volumetric fluorescence signals. Employing iACT, we uncover disrupted axonal projections within the mesolimbic dopaminergic (DA) circuits in 5xFAD mice. Subsequent characterization of DA neural circuits in 5xFAD mice revealed proximal axonal swelling and misrouting of distal axonal compartments in proximity to amyloid-beta plaques. Importantly, these structural anomalies in DA axons correlate with a marked reduction in DA release within the nucleus accumbens. Collectively, our findings highlight the efficacy of optical volumetric imaging with iACT in resolving intricate structural alterations in deep brain neural circuits. Furthermore, we unveil the compromised integrity of DA pathways, contributing to the underlying neuropathology of Alzheimer's disease. The iACT technique thus holds significant promise as a valuable asset for advancing our understanding of complex neurodegenerative disorders and may pave the way for targeted therapeutic interventions.
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Affiliation(s)
- Soonbong Baek
- Developmental Disorders & Rare Diseases Research Group, Korea Brain Research Institute, 61 Cheomdan-ro, Daegu, 41062, Republic of Korea
| | - Jaemyung Jang
- Developmental Disorders & Rare Diseases Research Group, Korea Brain Research Institute, 61 Cheomdan-ro, Daegu, 41062, Republic of Korea
| | - Hyun Jin Jung
- Developmental Disorders & Rare Diseases Research Group, Korea Brain Research Institute, 61 Cheomdan-ro, Daegu, 41062, Republic of Korea
| | - Hyeyoung Lee
- Division of Applied Bioengineering, Dong-eui University, Busanjin-gu, Busan, 47340, Republic of Korea
| | - Youngshik Choe
- Developmental Disorders & Rare Diseases Research Group, Korea Brain Research Institute, 61 Cheomdan-ro, Daegu, 41062, Republic of Korea.
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9
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Tsukui T, Wolters PJ, Sheppard D. Alveolar fibroblast lineage orchestrates lung inflammation and fibrosis. Nature 2024; 631:627-634. [PMID: 38987592 DOI: 10.1038/s41586-024-07660-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
Fibroblasts are present throughout the body and function to maintain tissue homeostasis. Recent studies have identified diverse fibroblast subsets in healthy and injured tissues1,2, but the origins and functional roles of injury-induced fibroblast lineages remain unclear. Here we show that lung-specialized alveolar fibroblasts take on multiple molecular states with distinct roles in facilitating responses to fibrotic lung injury. We generate a genetic tool that uniquely targets alveolar fibroblasts to demonstrate their role in providing niches for alveolar stem cells in homeostasis and show that loss of this niche leads to exaggerated responses to acute lung injury. Lineage tracing identifies alveolar fibroblasts as the dominant origin for multiple emergent fibroblast subsets sequentially driven by inflammatory and pro-fibrotic signals after injury. We identify similar, but not completely identical, fibroblast lineages in human pulmonary fibrosis. TGFβ negatively regulates an inflammatory fibroblast subset that emerges early after injury and stimulates the differentiation into fibrotic fibroblasts to elicit intra-alveolar fibrosis. Blocking the induction of fibrotic fibroblasts in the alveolar fibroblast lineage abrogates fibrosis but exacerbates lung inflammation. These results demonstrate the multifaceted roles of the alveolar fibroblast lineage in maintaining normal alveolar homeostasis and orchestrating sequential responses to lung injury.
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Affiliation(s)
- Tatsuya Tsukui
- Division of Pulmonary, Critical Care, Allergy and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Paul J Wolters
- Division of Pulmonary, Critical Care, Allergy and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Dean Sheppard
- Division of Pulmonary, Critical Care, Allergy and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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10
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Norris S, Hu JK, Shubin NH. Whole Tissue Imaging of Cellular Boundaries at Sub-Micron Resolutions for Automatic Cell Segmentation: Applications in Epithelial Bending of Ectodermal Appendages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600880. [PMID: 38979339 PMCID: PMC11230380 DOI: 10.1101/2024.06.26.600880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
For decades, biologists have relied on confocal microscopy to understand cellular morphology and the fine details of tissue structure. However, traditional confocal microscopy of tissues have limited penetration depths of light ∼ 100 µm due to tissue opaqueness. Researchers have, thus, developed tissue clearing protocols to be used with confocal microscopy, however, current clearing protocols are not compatible with labels of cell boundaries, especially at high enough resolution to precisely segment individual cells. In this work, we devise a method to retain markers of cell boundaries, and refractive index-match the tissues with water to enable tissue imaging at high magnification using long working distance water dipping objectives. The sub-micron resolution of these images allows us to automatically segment each individual cell using a trained neural network segmentation model. These segmented images can then be utilized to quantify cell properties and morphology of the entire three-dimensional tissue. As an example application, we first test our methodology on mandibles of mutant mice that express fluorescent proteins in their membranes. We then examine a non-model animal, the catshark, and explore the cellular properties of their dental lamina and dermal denticles, which are invaginating and evaginating ectodermal structures, respectively. We, thus, demonstrate that the technique presented here provides a powerful tool to quantify, in high-throughput, the 3D structures of cells and tissues during organ morphogenesis.
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11
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Sakurai J, Oka S, Higuchi Y, Ohsawa S, Fujimori T. Effects of blastocyst elongation and implantation chamber formation on the alignment of the embryonic axis and uterine axis in mice. Front Cell Dev Biol 2024; 12:1421222. [PMID: 38946796 PMCID: PMC11211524 DOI: 10.3389/fcell.2024.1421222] [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: 04/22/2024] [Accepted: 05/17/2024] [Indexed: 07/02/2024] Open
Abstract
Embryo implantation involves a series of events that bring the embryo and maternal tissues into contact to support post-implantation development in mammals. During implantation, alignment of the embryonic-abembryonic (E-Ab) axis of the blastocyst with the mesometrial-antimesometrial (M-AM) axis of the uterus precedes post-implantation embryonic development and placentation. In the present study, we observed the morphological changes in blastocysts and the endometrial luminal epithelium (LE) that occur during the alignment of the embryonic and the uterine axes. We found that at the time that the blastocysts attached to the LE at the mural trophectoderm, the embryonic axis was not aligned with the uterine axis. Alignment of the embryonic E-Ab axis with the uterine M-AM axis occurred after E4.0, and the embryo was significantly elongated during the process. The depth of the implantation chamber (IC) correlated with the degree of alignment, suggesting that elongated embryos are oriented along the M-AM axis during IC formation. Transplantation of the Concanavalin A (Con A)-coated beads induced IC formation, and the alignment of two Con A-coated beads present in the same IC in the M-AM direction suggested that elongated materials can align along the M-AM axis. These data suggest that an elongated shape of the embryo and IC formation coordinate the alignment of the embryonic and uterine axes.
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Affiliation(s)
- Jun Sakurai
- Division of Embryology, National Institute for Basic Biology, Okazaki, Japan
- Deapartment of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
| | - Sanae Oka
- Division of Embryology, National Institute for Basic Biology, Okazaki, Japan
| | - Yoko Higuchi
- Division of Embryology, National Institute for Basic Biology, Okazaki, Japan
| | - Sonoko Ohsawa
- Model Organisms Facility, Trans-Scale Biology Center, National Institute for Basic Biology, Okazaki, Japan
| | - Toshihiko Fujimori
- Division of Embryology, National Institute for Basic Biology, Okazaki, Japan
- Deapartment of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
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12
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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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13
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Nakayama Y, Fujiu K, Oshima T, Matsuda J, Sugita J, Matsubara TJ, Liu Y, Goto K, Kani K, Uchida R, Takeda N, Morita H, Xiao Y, Hayashi M, Maru Y, Hasumi E, Kojima T, Ishiguro S, Kijima Y, Yachie N, Yamazaki S, Yamamoto R, Kudo F, Nakanishi M, Iwama A, Fujiki R, Kaneda A, Ohara O, Nagai R, Manabe I, Komuro I. Heart failure promotes multimorbidity through innate immune memory. Sci Immunol 2024; 9:eade3814. [PMID: 38787963 DOI: 10.1126/sciimmunol.ade3814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
Patients with heart failure (HF) often experience repeated acute decompensation and develop comorbidities such as chronic kidney disease and frailty syndrome. Although this suggests pathological interaction among comorbidities, the mechanisms linking them are poorly understood. Here, we identified alterations in hematopoietic stem cells (HSCs) as a critical driver of recurrent HF and associated comorbidities. Bone marrow transplantation from HF-experienced mice resulted in spontaneous cardiac dysfunction and fibrosis in recipient mice, as well as increased vulnerability to kidney and skeletal muscle insults. HF enhanced the capacity of HSCs to generate proinflammatory macrophages. In HF mice, global chromatin accessibility analysis and single-cell RNA-seq showed that transforming growth factor-β (TGF-β) signaling was suppressed in HSCs, which corresponded with repressed sympathetic nervous activity in bone marrow. Transplantation of bone marrow from mice in which TGF-β signaling was inhibited similarly exacerbated cardiac dysfunction. Collectively, these results suggest that cardiac stress modulates the epigenome of HSCs, which in turn alters their capacity to generate cardiac macrophage subpopulations. This change in HSCs may be a common driver of repeated HF events and comorbidity by serving as a key carrier of "stress memory."
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Affiliation(s)
- Yukiteru Nakayama
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | - Katsuhito Fujiu
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
- Department of Advanced Cardiology, University of Tokyo, Tokyo, Japan
| | - Tsukasa Oshima
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | - Jun Matsuda
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | - Junichi Sugita
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | | | - Yuxiang Liu
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | - Kohsaku Goto
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | - Kunihiro Kani
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | - Ryoko Uchida
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
- Department of Advanced Cardiology, University of Tokyo, Tokyo, Japan
| | - Norifumi Takeda
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | - Hiroyuki Morita
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | - Yingda Xiao
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | - Michiko Hayashi
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | - Yujin Maru
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | - Eriko Hasumi
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | - Toshiya Kojima
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
| | - Soh Ishiguro
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yusuke Kijima
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Nozomu Yachie
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Synthetic Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Satoshi Yamazaki
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Laboratory of Stem Cell Therapy, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Ryo Yamamoto
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Fujimi Kudo
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Mio Nakanishi
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Iwama
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ryoji Fujiki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Ryozo Nagai
- Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Ichiro Manabe
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Issei Komuro
- Department of Cardiovascular Medicine, University of Tokyo, Tokyo, Japan
- International University of Health and Welfare, Tokyo, Japan
- Department of Frontier Cardiovascular Science, Graduate School of Tokyo, University of Tokyo, Tokyo, Japan
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14
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Lin YH, Wang LW, Chen YH, Chan YC, Hu SH, Wu SY, Chiang CS, Huang GJ, Yang SD, Chu SW, Wang KC, Lin CH, Huang PH, Cheng HJ, Chen BC, Chu LA. Revealing intact neuronal circuitry in centimeter-sized formalin-fixed paraffin-embedded brain. eLife 2024; 13:RP93212. [PMID: 38775133 PMCID: PMC11111220 DOI: 10.7554/elife.93212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024] Open
Abstract
Tissue-clearing and labeling techniques have revolutionized brain-wide imaging and analysis, yet their application to clinical formalin-fixed paraffin-embedded (FFPE) blocks remains challenging. We introduce HIF-Clear, a novel method for efficiently clearing and labeling centimeter-thick FFPE specimens using elevated temperature and concentrated detergents. HIF-Clear with multi-round immunolabeling reveals neuron circuitry regulating multiple neurotransmitter systems in a whole FFPE mouse brain and is able to be used as the evaluation of disease treatment efficiency. HIF-Clear also supports expansion microscopy and can be performed on a non-sectioned 15-year-old FFPE specimen, as well as a 3-month formalin-fixed mouse brain. Thus, HIF-Clear represents a feasible approach for researching archived FFPE specimens for future neuroscientific and 3D neuropathological analyses.
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Affiliation(s)
- Ya-Hui Lin
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua UniversityHsinchuTaiwan
- Brain Research Center, National Tsing Hua UniversityHsinchuTaiwan
| | - Li-Wen Wang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua UniversityHsinchuTaiwan
- Brain Research Center, National Tsing Hua UniversityHsinchuTaiwan
| | - Yen-Hui Chen
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - Yi-Chieh Chan
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua UniversityHsinchuTaiwan
| | - Shang-Hsiu Hu
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua UniversityHsinchuTaiwan
| | - Sheng-Yan Wu
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua UniversityHsinchuTaiwan
| | - Chi-Shiun Chiang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua UniversityHsinchuTaiwan
| | - Guan-Jie Huang
- Department of Physics, National Taiwan UniversityTaipeiTaiwan
| | - Shang-Da Yang
- Institute of Photonics Technologies, National Tsing Hua UniversityHsinchuTaiwan
| | - Shi-Wei Chu
- Department of Physics, National Taiwan UniversityTaipeiTaiwan
| | - Kuo-Chuan Wang
- Department of Neurosurgery, National Taiwan University HospitalTaipeiTaiwan
| | - Chin-Hsien Lin
- Department of Neurosurgery, National Taiwan University HospitalTaipeiTaiwan
| | - Pei-Hsin Huang
- Department of Pathology, National Taiwan University HospitalTaipeiTaiwan
| | | | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia SinicaTaipeiTaiwan
| | - Li-An Chu
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua UniversityHsinchuTaiwan
- Brain Research Center, National Tsing Hua UniversityHsinchuTaiwan
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15
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Zheng W, Mu H, Chen Z, Liu J, Xia D, Cheng Y, Jing Q, Lau PM, Tang J, Bi GQ, Wu F, Wang H. NEATmap: a high-efficiency deep learning approach for whole mouse brain neuronal activity trace mapping. Natl Sci Rev 2024; 11:nwae109. [PMID: 38831937 PMCID: PMC11145917 DOI: 10.1093/nsr/nwae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/26/2024] [Accepted: 02/25/2024] [Indexed: 06/05/2024] Open
Abstract
Quantitative analysis of activated neurons in mouse brains by a specific stimulation is usually a primary step to locate the responsive neurons throughout the brain. However, it is challenging to comprehensively and consistently analyze the neuronal activity trace in whole brains of a large cohort of mice from many terabytes of volumetric imaging data. Here, we introduce NEATmap, a deep learning-based high-efficiency, high-precision and user-friendly software for whole-brain neuronal activity trace mapping by automated segmentation and quantitative analysis of immunofluorescence labeled c-Fos+ neurons. We applied NEATmap to study the brain-wide differentiated neuronal activation in response to physical and psychological stressors in cohorts of mice.
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Affiliation(s)
- Weijie Zheng
- AHU-IAI AI Joint Laboratory, Anhui University, Hefei 230039, China
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Huawei Mu
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Zhiyi Chen
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Jiajun Liu
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Debin Xia
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Yuxiao Cheng
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Qi Jing
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Pak-Ming Lau
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jin Tang
- AHU-IAI AI Joint Laboratory, Anhui University, Hefei 230039, China
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
| | - Guo-Qiang Bi
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Feng Wu
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Hao Wang
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
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16
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Gao P, Rivera M, Lin X, Holmes TC, Zhao H, Xu X. Immunolabeling-compatible PEGASOS tissue clearing for high-resolution whole mouse brain imaging. Front Neural Circuits 2024; 18:1345692. [PMID: 38694272 PMCID: PMC11061518 DOI: 10.3389/fncir.2024.1345692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/13/2024] [Indexed: 05/04/2024] Open
Abstract
Novel brain clearing methods revolutionize imaging by increasing visualization throughout the brain at high resolution. However, combining the standard tool of immunostaining targets of interest with clearing methods has lagged behind. We integrate whole-mount immunostaining with PEGASOS tissue clearing, referred to as iPEGASOS (immunostaining-compatible PEGASOS), to address the challenge of signal quenching during clearing processes. iPEGASOS effectively enhances molecular-genetically targeted fluorescent signals that are otherwise compromised during conventional clearing procedures. Additionally, we demonstrate the utility of iPEGASOS for visualizing neurochemical markers or viral labels to augment visualization that transgenic mouse lines cannot provide. Our study encompasses three distinct applications, each showcasing the versatility and efficacy of this approach. We employ whole-mount immunostaining to enhance molecular signals in transgenic reporter mouse lines to visualize the whole-brain spatial distribution of specific cellular populations. We also significantly improve the visualization of neural circuit connections by enhancing signals from viral tracers injected into the brain. Last, we show immunostaining without genetic markers to selectively label beta-amyloid deposits in a mouse model of Alzheimer's disease, facilitating the comprehensive whole-brain study of pathological features.
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Affiliation(s)
- Pan Gao
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Matthew Rivera
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Xiaoxiao Lin
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Todd C. Holmes
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, United States
- Center for Neural Circuit Mapping, University of California, Irvine, Irvine, CA, United States
| | - Hu Zhao
- Chinese Institute for Brain Research, Beijing, China
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
- Center for Neural Circuit Mapping, University of California, Irvine, Irvine, CA, United States
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17
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Takeshita N, Sakaki S, Saba R, Inoue S, Nishikawa K, Ueyama A, Nakajima Y, Matsuo K, Shigeta M, Kobayashi D, Yamazaki H, Yamada K, Iehara T, Yashiro K. Acto3D: an open-source user-friendly volume rendering software for high-resolution 3D fluorescence imaging in biology. Development 2024; 151:dev202550. [PMID: 38657972 DOI: 10.1242/dev.202550] [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: 11/16/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024]
Abstract
Advances in fluorescence microscopy and tissue-clearing have revolutionised 3D imaging of fluorescently labelled tissues, organs and embryos. However, the complexity and high cost of existing software and computing solutions limit their widespread adoption, especially by researchers with limited resources. Here, we present Acto3D, an open-source software, designed to streamline the generation and analysis of high-resolution 3D images of targets labelled with multiple fluorescent probes. Acto3D provides an intuitive interface for easy 3D data import and visualisation. Although Acto3D offers straightforward 3D viewing, it performs all computations explicitly, giving users detailed control over the displayed images. Leveraging an integrated graphics processing unit, Acto3D deploys all pixel data to system memory, reducing visualisation latency. This approach facilitates accurate image reconstruction and efficient data processing in 3D, eliminating the need for expensive high-performance computers and dedicated graphics processing units. We have also introduced a method for efficiently extracting lumen structures in 3D. We have validated Acto3D by imaging mouse embryonic structures and by performing 3D reconstruction of pharyngeal arch arteries while preserving fluorescence information. Acto3D is a cost-effective and efficient platform for biological research.
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Affiliation(s)
- Naoki Takeshita
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Shinichiro Sakaki
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Rie Saba
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
- Department of Radiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Satoshi Inoue
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kosuke Nishikawa
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Atsuko Ueyama
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Yoshiro Nakajima
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kazuhiko Matsuo
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Masaki Shigeta
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Daisuke Kobayashi
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Hideya Yamazaki
- Department of Radiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kei Yamada
- Department of Radiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Tomoko Iehara
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kenta Yashiro
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
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18
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Takahashi-Yamashiro K, Miyazono K. Tissue clearing method in visualization of cancer progression and metastasis. Ups J Med Sci 2024; 129:10634. [PMID: 38716075 PMCID: PMC11075440 DOI: 10.48101/ujms.v129.10634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 03/07/2024] [Indexed: 05/24/2024] Open
Abstract
Since various imaging modalities have been developed, cancer metastasis can be detected from an early stage. However, limitations still exist, especially in terms of spatial resolution. Tissue-clearing technology has emerged as a new imaging modality in cancer research, which has been developed and utilized for a long time mainly in neuroscience field. This method enables us to detect cancer metastatic foci with single-cell resolution at whole mouse body/organ level. On top of that, 3D images of cancer metastasis of whole mouse organs make it easy to understand their characteristics. Recently, further applications of tissue clearing methods were reported in combination with reporter systems, labeling, and machine learning. In this review, we would like to provide an overview of this technique and current applications in cancer research and discuss their potentials and limitations.
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Affiliation(s)
- Kei Takahashi-Yamashiro
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton, Alberta, Canada
| | - Kohei Miyazono
- Department of Applied Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Cancer Invasion and Metastasis, Institute for Medical Sciences, RIKEN, Yokohama City, Kanagawa, Japan
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19
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Bishop KW, Erion Barner LA, Han Q, Baraznenok E, Lan L, Poudel C, Gao G, Serafin RB, Chow SSL, Glaser AK, Janowczyk A, Brenes D, Huang H, Miyasato D, True LD, Kang S, Vaughan JC, Liu JTC. An end-to-end workflow for nondestructive 3D pathology. Nat Protoc 2024; 19:1122-1148. [PMID: 38263522 DOI: 10.1038/s41596-023-00934-4] [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: 07/27/2023] [Accepted: 10/23/2023] [Indexed: 01/25/2024]
Abstract
Recent advances in 3D pathology offer the ability to image orders of magnitude more tissue than conventional pathology methods while also providing a volumetric context that is not achievable with 2D tissue sections, and all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis, however, is not trivial and requires careful attention to a series of details during tissue preparation, imaging and initial data processing, as well as iterative optimization of the entire process. Here, we provide an end-to-end procedure covering all aspects of a 3D pathology workflow (using light-sheet microscopy as an illustrative imaging platform) with sufficient detail to perform well-controlled preclinical and clinical studies. Although 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol focuses on the use of a fluorescent analog of hematoxylin and eosin, which remains the most common stain used for gold-standard pathological reports. We present our guidelines for a broad range of end users (e.g., biologists, clinical researchers and engineers) in a simple format. The end-to-end workflow requires 3-6 d to complete, bearing in mind that data analysis may take longer.
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Affiliation(s)
- Kevin W Bishop
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | - Qinghua Han
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Elena Baraznenok
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Lydia Lan
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Chetan Poudel
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Gan Gao
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Robert B Serafin
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Sarah S L Chow
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Adam K Glaser
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Emory University, Atlanta, GA, USA
- Department of Oncology, Division of Precision Oncology, University Hospital of Geneva, Geneva, Switzerland
- Department of Diagnostics, Division of Clinical Pathology, University Hospital of Geneva, Geneva, Switzerland
| | - David Brenes
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Hongyi Huang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Dominie Miyasato
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Lawrence D True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Soyoung Kang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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20
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Mai H, Luo J, Hoeher L, Al-Maskari R, Horvath I, Chen Y, Kofler F, Piraud M, Paetzold JC, Modamio J, Todorov M, Elsner M, Hellal F, Ertürk A. Whole-body cellular mapping in mouse using standard IgG antibodies. Nat Biotechnol 2024; 42:617-627. [PMID: 37430076 PMCID: PMC11021200 DOI: 10.1038/s41587-023-01846-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 05/26/2023] [Indexed: 07/12/2023]
Abstract
Whole-body imaging techniques play a vital role in exploring the interplay of physiological systems in maintaining health and driving disease. We introduce wildDISCO, a new approach for whole-body immunolabeling, optical clearing and imaging in mice, circumventing the need for transgenic reporter animals or nanobody labeling and so overcoming existing technical limitations. We identified heptakis(2,6-di-O-methyl)-β-cyclodextrin as a potent enhancer of cholesterol extraction and membrane permeabilization, enabling deep, homogeneous penetration of standard antibodies without aggregation. WildDISCO facilitates imaging of peripheral nervous systems, lymphatic vessels and immune cells in whole mice at cellular resolution by labeling diverse endogenous proteins. Additionally, we examined rare proliferating cells and the effects of biological perturbations, as demonstrated in germ-free mice. We applied wildDISCO to map tertiary lymphoid structures in the context of breast cancer, considering both primary tumor and metastases throughout the mouse body. An atlas of high-resolution images showcasing mouse nervous, lymphatic and vascular systems is accessible at http://discotechnologies.org/wildDISCO/atlas/index.php .
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Affiliation(s)
- Hongcheng Mai
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Medical Centre of the University of Munich, Ludwig-Maximilians University of Munich, Munich, Germany
- Munich Medical Research School, Munich, Germany
- Deep Piction GmbH, Munich, Germany
| | - Jie Luo
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Medical Centre of the University of Munich, Ludwig-Maximilians University of Munich, Munich, Germany
- Deep Piction GmbH, Munich, Germany
| | - Luciano Hoeher
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
| | - Rami Al-Maskari
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
| | - Izabela Horvath
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
| | - Ying Chen
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Medical Centre of the University of Munich, Ludwig-Maximilians University of Munich, Munich, Germany
- Faculty of Medicine, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Florian Kofler
- Helmholtz Al, Helmholtz Center Munich, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Munich, Germany
- TranslaTUM - Central Institute for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Marie Piraud
- Helmholtz Al, Helmholtz Center Munich, Neuherberg, Germany
| | - Johannes C Paetzold
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- Department of Computing, Imperial College London, London, UK
| | - Jennifer Modamio
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
| | - Mihail Todorov
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Medical Centre of the University of Munich, Ludwig-Maximilians University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Markus Elsner
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
| | - Farida Hellal
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Medical Centre of the University of Munich, Ludwig-Maximilians University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Ali Ertürk
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Center Munich, Neuherberg, Germany.
- Institute for Stroke and Dementia Research, Medical Centre of the University of Munich, Ludwig-Maximilians University of Munich, Munich, Germany.
- Deep Piction GmbH, Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
- Graduate School of Neuroscience (GSN), Munich, Germany.
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21
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Yoshikawa AL, Omura T, Takahashi-Kanemitsu A, Susaki EA. Blueprints from plane to space: outlook of next-generation three-dimensional histopathology. Cancer Sci 2024; 115:1029-1038. [PMID: 38316137 PMCID: PMC11006986 DOI: 10.1111/cas.16095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/02/2024] [Accepted: 01/16/2024] [Indexed: 02/07/2024] Open
Abstract
Here, we summarize the literature relevant to recent advances in three-dimensional (3D) histopathology in relation to clinical oncology, highlighting serial sectioning, tissue clearing, light-sheet microscopy, and digital image analysis with artificial intelligence. We look forward to a future where 3D histopathology expands our understanding of human pathophysiology and improves patient care through cross-disciplinary collaboration and innovation.
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Affiliation(s)
- Akira Leon Yoshikawa
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Pathology Informatics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Pathology, Kameda Medical Center, Chiba, Japan
| | - Takaki Omura
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Atsushi Takahashi-Kanemitsu
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Etsuo A Susaki
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
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22
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Sakamoto DM, Tamura I, Yi B, Hasegawa S, Saito Y, Yamada N, Takakusagi Y, Kubota SI, Kobayashi M, Harada H, Hanaoka K, Taki M, Nangaku M, Tainaka K, Sando S. Whole-Body and Whole-Organ 3D Imaging of Hypoxia Using an Activatable Covalent Fluorescent Probe Compatible with Tissue Clearing. ACS NANO 2024; 18:5167-5179. [PMID: 38301048 DOI: 10.1021/acsnano.3c12716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Elucidation of biological phenomena requires imaging of microenvironments in vivo. Although the seamless visualization of in vivo hypoxia from the level of whole-body to single-cell has great potential to discover unknown phenomena in biological and medical fields, no methodology for achieving it has been established thus far. Here, we report the whole-body and whole-organ imaging of hypoxia, an important microenvironment, at single-cell resolution using activatable covalent fluorescent probes compatible with tissue clearing. We initially focused on overcoming the incompatibility of fluorescent dyes and refractive index matching solutions (RIMSs), which has greatly hindered the development of fluorescent molecular probes in the field of tissue clearing. The fluorescent dyes compatible with RIMS were then incorporated into the development of activatable covalent fluorescent probes for hypoxia. We combined the probes with tissue clearing, achieving comprehensive single-cell-resolution imaging of hypoxia in a whole mouse body and whole organs.
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Affiliation(s)
- Daichi M Sakamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Iori Tamura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Bo Yi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Sho Hasegawa
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Yutaro Saito
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Naoki Yamada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yoichi Takakusagi
- Quantum Hyperpolarized MRI Team, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba-city 263-8555, Japan
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba-city 263-8555, Japan
| | - Shimpei I Kubota
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Kita-15, Nishi-7, Kita-ku, Sapporo, Hokkaido 060-0815, Japan
| | - Minoru Kobayashi
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Genome Dynamics, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Harada
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Genome Dynamics, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kenjiro Hanaoka
- Division of Analytical Chemistry for Drug Discovery, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Masayasu Taki
- Institute of Transformative Bio-Molecules, Nagoya University, Furo, Chikusa, Nagoya 464-8601, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata 951-8585, Japan
- Gftd DeSci, Gftd DAO, Nishikawa Building, 20 Kikuicho, Shinjuku-ku, Tokyo 162-0044, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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23
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Nonaka H, Sakamoto S, Shiraiwa K, Ishikawa M, Tamura T, Okuno K, Kondo T, Kiyonaka S, Susaki EA, Shimizu C, Ueda HR, Kakegawa W, Arai I, Yuzaki M, Hamachi I. Bioorthogonal chemical labeling of endogenous neurotransmitter receptors in living mouse brains. Proc Natl Acad Sci U S A 2024; 121:e2313887121. [PMID: 38294939 PMCID: PMC10861872 DOI: 10.1073/pnas.2313887121] [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: 08/12/2023] [Accepted: 12/16/2023] [Indexed: 02/02/2024] Open
Abstract
Neurotransmitter receptors are essential components of synapses for communication between neurons in the brain. Because the spatiotemporal expression profiles and dynamics of neurotransmitter receptors involved in many functions are delicately governed in the brain, in vivo research tools with high spatiotemporal resolution for receptors in intact brains are highly desirable. Covalent labeling by chemical reaction (chemical labeling) of proteins without genetic manipulation is now a powerful method for analyzing receptors in vitro. However, selective target receptor labeling in the brain has not yet been achieved. This study shows that ligand-directed alkoxyacylimidazole (LDAI) chemistry can be used to selectively tether synthetic probes to target endogenous receptors in living mouse brains. The reactive LDAI reagents with negative charges were found to diffuse well over the whole brain and could selectively label target endogenous receptors, including AMPAR, NMDAR, mGlu1, and GABAAR. This simple and robust labeling protocol was then used for various applications: three-dimensional spatial mapping of endogenous receptors in the brains of healthy and disease-model mice; multi-color receptor imaging; and pulse-chase analysis of the receptor dynamics in postnatal mouse brains. Here, results demonstrated that bioorthogonal receptor modification in living animal brains may provide innovative molecular tools that contribute to the in-depth understanding of complicated brain functions.
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Affiliation(s)
- Hiroshi Nonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
| | - Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
| | - Kazuki Shiraiwa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Mamoru Ishikawa
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
| | - Kyohei Okuno
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Takumi Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya464-8603, Japan
| | - Shigeki Kiyonaka
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya464-8603, Japan
| | - Etsuo A. Susaki
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo113-8421, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
| | - Chika Shimizu
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
| | - Wataru Kakegawa
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
- Department of Neurophysiology, Keio University School of Medicine, Tokyo160-8582, Japan
| | - Itaru Arai
- Department of Neurophysiology, Keio University School of Medicine, Tokyo160-8582, Japan
| | - Michisuke Yuzaki
- Department of Neurophysiology, Keio University School of Medicine, Tokyo160-8582, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
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24
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Liu JTC, Chow SSL, Colling R, Downes MR, Farré X, Humphrey P, Janowczyk A, Mirtti T, Verrill C, Zlobec I, True LD. Engineering the future of 3D pathology. J Pathol Clin Res 2024; 10:e347. [PMID: 37919231 PMCID: PMC10807588 DOI: 10.1002/cjp2.347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/06/2023] [Accepted: 10/15/2023] [Indexed: 11/04/2023]
Abstract
In recent years, technological advances in tissue preparation, high-throughput volumetric microscopy, and computational infrastructure have enabled rapid developments in nondestructive 3D pathology, in which high-resolution histologic datasets are obtained from thick tissue specimens, such as whole biopsies, without the need for physical sectioning onto glass slides. While 3D pathology generates massive datasets that are attractive for automated computational analysis, there is also a desire to use 3D pathology to improve the visual assessment of tissue histology. In this perspective, we discuss and provide examples of potential advantages of 3D pathology for the visual assessment of clinical specimens and the challenges of dealing with large 3D datasets (of individual or multiple specimens) that pathologists have not been trained to interpret. We discuss the need for artificial intelligence triaging algorithms and explainable analysis methods to assist pathologists or other domain experts in the interpretation of these novel, often complex, large datasets.
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Affiliation(s)
- Jonathan TC Liu
- Department of Mechanical EngineeringUniversity of WashingtonSeattleWAUSA
- Department of Laboratory Medicine & PathologyUniversity of Washington School of MedicineSeattleUSA
- Department of BioengineeringUniversity of WashingtonSeattleUSA
| | - Sarah SL Chow
- Department of Mechanical EngineeringUniversity of WashingtonSeattleWAUSA
| | | | | | | | - Peter Humphrey
- Department of UrologyYale School of MedicineNew HavenCTUSA
| | - Andrew Janowczyk
- Wallace H Coulter Department of Biomedical EngineeringEmory University and Georgia Institute of TechnologyAtlantaGAUSA
- Geneva University HospitalsGenevaSwitzerland
| | - Tuomas Mirtti
- Helsinki University Hospital and University of HelsinkiHelsinkiFinland
- Emory University School of MedicineAtlantaGAUSA
| | - Clare Verrill
- John Radcliffe HospitalUniversity of OxfordOxfordUK
- NIHR Oxford Biomedical Research CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Inti Zlobec
- Institute for Tissue Medicine and PathologyUniversity of BernBernSwitzerland
| | - Lawrence D True
- Department of Laboratory Medicine & PathologyUniversity of Washington School of MedicineSeattleUSA
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Chen L, Meng J, Zhou Y, Zhao F, Ma Y, Feng W, Chen X, jin J, Gao S, Liu J, Zhang M, Liu A, Hong Z, Tang J, Kuang D, Huang L, Zhang Y, Fei P. Efficient 3D imaging and pathological analysis of the human lymphoma tumor microenvironment using light-sheet immunofluorescence microscopy. Theranostics 2024; 14:406-419. [PMID: 38164148 PMCID: PMC10750216 DOI: 10.7150/thno.86221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/26/2023] [Indexed: 01/03/2024] Open
Abstract
Rationale: The composition and spatial structure of the lymphoma tumor microenvironment (TME) provide key pathological insights for tumor survival and growth, invasion and metastasis, and resistance to immunotherapy. However, the 3D lymphoma TME has not been well studied owing to the limitations of current imaging techniques. In this work, we take full advantage of a series of new techniques to enable the first 3D TME study in intact lymphoma tissue. Methods: Diverse cell subtypes in lymphoma tissues were tagged using a multiplex immunofluorescence labeling technique. To optically clarify the entire tissue, immunolabeling-enabled three-dimensional imaging of solvent-cleared organs (iDISCO+), clear, unobstructed brain imaging cocktails and computational analysis (CUBIC) and stabilization to harsh conditions via intramolecular epoxide linkages to prevent degradation (SHIELD) were comprehensively compared with the ultimate dimensional imaging of solvent-cleared organs (uDISCO) approach selected for clearing lymphoma tissues. A Bessel-beam light-sheet fluorescence microscope (B-LSFM) was developed to three-dimensionally image the clarified tissues at high speed and high resolution. A customized MATLAB program was used to quantify the number and colocalization of the cell subtypes based on the acquired multichannel 3D images. By combining these cutting-edge methods, we successfully carried out high-efficiency 3D visualization and high-content cellular analyses of the lymphoma TME. Results: Several antibodies, including CD3, CD8, CD20, CD68, CD163, CD14, CD15, FOXP3 and Ki67, were screened for labeling the TME in lymphoma tumors. The 3D imaging results of the TME from three types of lymphoma, reactive lymphocytic hyperplasia (RLN), diffuse large B-cell lymphoma (DLBCL), and angioimmunoblastic T-cell lymphoma (AITL), were quantitatively analyzed, and their cell number, localization, and spatial correlation were comprehensively revealed. Conclusion: We present an advanced imaging-based method for efficient 3D visualization and high-content cellular analysis of the lymphoma TME, rendering it a valuable tool for tumor pathological diagnosis and other clinical research.
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Affiliation(s)
- Liting Chen
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiao Meng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hematology Department, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Yao Zhou
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Zhao
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Yifan Ma
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Wenyang Feng
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Xingyu Chen
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Jin jin
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shimeng Gao
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Jianchao Liu
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Man Zhang
- Hematology Department, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Aichun Liu
- Hematology Department, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Zhenya Hong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Tang
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Dong Kuang
- Department of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yicheng Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Fei
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
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McKenzie AT, Nnadi O, Slagell KD, Thorn EL, Farrell K, Crary JF. Fluid preservation in brain banking: a review. FREE NEUROPATHOLOGY 2024; 5:5-10. [PMID: 38690035 PMCID: PMC11058410 DOI: 10.17879/freeneuropathology-2024-5373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Fluid preservation is nearly universally used in brain banking to store fixed tissue specimens for future research applications. However, the effects of long-term immersion on neural circuitry and biomolecules are not well characterized. As a result, there is a need to synthesize studies investigating fluid preservation of brain tissue. We searched PubMed and other databases to identify studies measuring the effects of fluid preservation in nervous system tissue. We categorized studies based on the fluid preservative used: formaldehyde solutions, buffer solutions, alcohol solutions, storage after tissue clearing, and cryoprotectant solutions. We identified 91 studies containing 197 independent observations of the effects of long-term storage on cellular morphology. Most studies did not report any significant alterations due to long-term storage. When present, the most frequent alteration was decreased antigenicity, commonly attributed to progressive crosslinking by aldehydes that renders biomolecules increasingly inaccessible over time. To build a mechanistic understanding, we discuss biochemical aspects of long-term fluid preservation. A subset of lipids appears to be chemical altered or extracted over time due to incomplete retention in the crosslinked gel. Alternative storage fluids mitigate the problem of antigen masking but have not been extensively characterized and may have other downsides. We also compare fluid preservation to cryopreservation, paraffin embedding, and resin embedding. Overall, existing evidence suggests that fluid preservation provides maintenance of neural architecture for decades, including precise structural details. However, to avoid the well-established problem of overfixation caused by storage in high concentration formaldehyde solutions, fluid preservation procedures can use an initial fixation step followed by an alternative long-term storage fluid. Further research is warranted on optimizing protocols and characterizing the generalizability of the storage artifacts that have been identified.
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Affiliation(s)
| | - Oge Nnadi
- Brain Preservation Foundation, Ashburn, Virginia, USA
| | - Kat D. Slagell
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emma L. Thorn
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kurt Farrell
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John F. Crary
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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27
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Phillips EH, Bindokas VP, Jung D, Teamer J, Kitajewski JK, Solaro RJ, Wolska BM, Lee SSY. Three-dimensional spatial quantitative analysis of cardiac lymphatics in the mouse heart. Microcirculation 2023; 30:e12826. [PMID: 37605603 PMCID: PMC10592199 DOI: 10.1111/micc.12826] [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: 02/10/2023] [Revised: 07/04/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023]
Abstract
OBJECTIVE Three-dimensional (3D) microscopy and image data analysis are necessary for studying the morphology of cardiac lymphatic vessels (LyVs) and their association with other cell types. We aimed to develop a methodology for 3D multiplexed lightsheet microscopy and highly sensitive and quantitative image analysis to identify pathological remodeling in the 3D morphology of LyVs in young adult mouse hearts with familial hypertrophic cardiomyopathy (HCM). METHODS We developed a 3D lightsheet microscopy workflow providing a quick turn-around (as few as 5-6 days), multiplex fluorescence detection, and preservation of LyV structure and epitope markers. Hearts from non-transgenic and transgenic (TG) HCM mice were arrested in diastole, retrograde perfused, immunolabeled, optically cleared, and imaged. We built an image-processing pipeline to quantify LyV morphological parameters at the chamber and branch levels. RESULTS Chamber-specific pathological alterations of LyVs were identified, and significant changes were seen in the right atrium (RA). TG hearts had a higher volume percent of ER-TR7+ fibroblasts and reticular fibers. In the RA, we found associations between ER-TR7+ volume percent and both LyV segment density and median diameter. CONCLUSIONS This workflow and study enabled multi-scale analysis of pathological changes in cardiac LyVs of young adult mice, inviting ideas for research on LyVs in cardiac disease.
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Affiliation(s)
- Evan H. Phillips
- Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 S. Wood, Chicago, IL, USA
- Department of Physiology and Biophysics, University of Illinois Chicago, 835 S. Wolcott, Chicago, IL, USA
| | - Vytautas P. Bindokas
- Integrated Light Microscopy Facility, The University of Chicago, 900 E. 57, Chicago, IL, USA
| | - Dahee Jung
- Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 S. Wood, Chicago, IL, USA
| | - Jay Teamer
- Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 S. Wood, Chicago, IL, USA
| | - Jan K. Kitajewski
- Department of Physiology and Biophysics, University of Illinois Chicago, 835 S. Wolcott, Chicago, IL, USA
| | - R. John Solaro
- Department of Physiology and Biophysics, University of Illinois Chicago, 835 S. Wolcott, Chicago, IL, USA
| | - Beata M. Wolska
- Department of Physiology and Biophysics, University of Illinois Chicago, 835 S. Wolcott, Chicago, IL, USA
- Department of Medicine, Division of Cardiology, Center for Cardiovascular Research, University of Illinois Chicago, 840 S. Wood, Chicago, IL, USA
| | - Steve Seung-Young Lee
- Department of Pharmaceutical Sciences, University of Illinois Chicago, 833 S. Wood, Chicago, IL, USA
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28
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Zhang Y, Liu G, Li X, Gong H, Luo Q, Yang X. On-line clearing and staining method for the efficient optical imaging of large volume samples at the cellular resolution. BIOMEDICAL OPTICS EXPRESS 2023; 14:4800-4813. [PMID: 37791250 PMCID: PMC10545182 DOI: 10.1364/boe.499115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 10/05/2023]
Abstract
Optical microscopy is a powerful tool for exploring the structure and function of organisms. However, the three-dimensional (3D) imaging of large volume samples is time-consuming and difficult. In this manuscript, we described an on-line clearing and staining method for efficient imaging of large volume samples at the cellular resolution. The optimized cocktail can increase staining and imaging depth to reduce the sectioning and scanning time, more than doubling the operational efficiency of the system. Using this method, we demonstrated the rapid acquisition of Aβ plaques in whole mouse brain and obtained a complete set of cytoarchitecture images of an adult porcine hemisphere at 1.625 × 1.625 × 10 µm3 voxel resolution for about 49 hours.
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Affiliation(s)
- Yunfei Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Guangcai Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiangning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, 215123, China
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, 215123, China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, 215123, China
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, China
| | - Xiaoquan Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, 215123, China
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29
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Bishop KW, Barner LAE, Han Q, Baraznenok E, Lan L, Poudel C, Gao G, Serafin RB, Chow SS, Glaser AK, Janowczyk A, Brenes D, Huang H, Miyasato D, True LD, Kang S, Vaughan JC, Liu JT. An end-to-end workflow for non-destructive 3D pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551845. [PMID: 37577615 PMCID: PMC10418226 DOI: 10.1101/2023.08.03.551845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Recent advances in 3D pathology offer the ability to image orders-of-magnitude more tissue than conventional pathology while providing a volumetric context that is lacking with 2D tissue sections, all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis is non-trivial, requiring careful attention to many details regarding tissue preparation, imaging, and data/image processing in an iterative process. Here we provide an end-to-end protocol covering all aspects of a 3D pathology workflow (using light-sheet microscopy as an illustrative imaging platform) with sufficient detail to perform well-controlled preclinical and clinical studies. While 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol will focus on a fluorescent analog of hematoxylin and eosin (H&E), which remains the most common stain for gold-standard diagnostic determinations. We present our guidelines for a broad range of end-users (e.g., biologists, clinical researchers, and engineers) in a simple tutorial format.
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Affiliation(s)
- Kevin W. Bishop
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | | | - Qinghua Han
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Elena Baraznenok
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Lydia Lan
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Chetan Poudel
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Gan Gao
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Robert B. Serafin
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Sarah S.L. Chow
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Adam K. Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
- Department of Oncology, Division of Precision Oncology, University Hospital of Geneva, Geneva, Switzerland
- Department of Clinical Pathology, Division of Clinical Pathology, University Hospital of Geneva, Geneva, Switzerland
| | - David Brenes
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Hongyi Huang
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Dominie Miyasato
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Soyoung Kang
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA
| | - Jonathan T.C. Liu
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
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30
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Ikeda E, Shinozaki S, Sakaguchi M, Sano N, Kabasawa S, Kanno A, Ando K, Yokoyama K, Tamada K, Onodera H, Yamamoto H, Fukushima N. The Ki67 index evaluation of pancreatic neuroendocrine tumors using 3D immunohistochemistry in small tissue specimens. Pancreatology 2023; 23:537-542. [PMID: 37301696 DOI: 10.1016/j.pan.2023.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/09/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND /Objectives: This study aimed to evaluate the usefulness of three-dimensional (3D) immunohistochemistry for the Ki67 index of small tissue specimens of pancreatic neuroendocrine tumor (PanNET). METHODS Clinicopathological materials from 17 patients with PanNET who underwent surgical resection at Jichi Medical University Hospital were analyzed. We compared the Ki67 index of endoscopic ultrasonography-fine-needle aspiration biopsy (EUS-FNAB) specimens, surgical specimens, and small tissue specimens hollowed from paraffin blocks of surgical specimens that were substituted for EUS-FNAB specimens ("sub-FNAB"). The sub-FNAB specimens were optically cleared using LUCID (IlLUmination of Cleared organs to IDentify target molecules) and analyzed using 3D immunohistochemistry. RESULTS The median Ki67 index in FNAB, sub-FNAB, and surgical specimens with conventional immunohistochemistry were 1.2% (0.7-5.0), 2.0% (0.5-14.6), and 5.4% (1.0-19.4), respectively. The median Ki67 index in sub-FNAB specimens with tissue clearing was calculated separately using the total number of cells on multiple images ("multiple slice"), with the image of the fewest positive cells ("coldspot"), and with the image of most positive cells ("hotspot"), which were 2.7% (0.2-8.2), 0.8% (0-4.8), and 5.5% (2.3-12.4), respectively. PanNET grade evaluated for the hotspot of the surgical specimens was significantly more consistent with those of the hotspot than multiple images of sub-FNAB specimens (16/17 vs. 10/17, p = 0.015). Hotspot evaluation using 3D immunohistochemistry of the sub-FNAB specimens showed agreement with the assessment of the surgical specimens (Kappa coefficient: 0.82). CONCLUSIONS Tissue clearing and 3D immunohistochemistry for the Ki67 index can potentially improve the preoperative evaluation of EUS-FNAB specimens of PanNET in routine clinical practice.
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Affiliation(s)
- Eriko Ikeda
- Department of Pathology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan; Department of Medicine, Division of Gastroenterology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan
| | - Satoshi Shinozaki
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan; Shinozaki Medical Clinic, 6-1-13 Kiyoharadai, Utsunomiya, 321-3223, Japan
| | - Mio Sakaguchi
- Department of Pathology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan
| | - Naoki Sano
- Department of Pathology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan
| | - Shin Kabasawa
- Department of Pathology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan
| | - Atsushi Kanno
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan
| | - Kozue Ando
- Department of Pathology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan; Department of Medicine, Division of Gastroenterology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan
| | - Kensuke Yokoyama
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan
| | - Kiichi Tamada
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan
| | - Hiroshi Onodera
- Photon Science Center, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-0033, Japan
| | - Hironori Yamamoto
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan
| | - Noriyoshi Fukushima
- Department of Pathology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan.
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31
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Landry CR, Yip MC, Zhou Y, Niu W, Wang Y, Yang B, Wen Z, Forest CR. Electrophysiological and morphological characterization of single neurons in intact human brain organoids. J Neurosci Methods 2023; 394:109898. [PMID: 37236404 PMCID: PMC10483933 DOI: 10.1016/j.jneumeth.2023.109898] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/12/2023] [Accepted: 05/20/2023] [Indexed: 05/28/2023]
Abstract
Brain organoids represent a new model system for studying developmental human neurophysiology. Methods for studying the electrophysiology and morphology of single neurons in organoids require acute slices or dissociated cultures. While these methods have advantages (e.g., visual access, ease of experimentation), they risk damaging cells and circuits present in the intact organoid. To access single cells within intact organoid circuits, we have demonstrated a method for fixturing and performing whole cell patch clamp recording from intact brain organoids using both manual and automated tools. We demonstrate applied electrophysiology methods development followed by an integration of electrophysiology with reconstructing the morphology of the neurons within the brain organoid using dye filling and tissue clearing. We found that whole cell patch clamp recordings could be achieved both on the surface and within the interior of intact human brain organoids using both manual and automated methods. Manual experiments were higher yield (53 % whole cell success rate manual, 9 % whole cell success rate automated), but automated experiments were more efficient (30 patch attempts per day automated, 10 patch attempts per day manual). Using these methods, we performed an unbiased survey of cells within human brain organoids between 90 and 120 days in vitro (DIV) and present preliminary data on morphological and electrical diversity in human brain organoids. The further development of intact brain organoid patch clamp methods could be broadly applicable to studies of cellular, synaptic, and circuit-level function in the developing human brain.
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Affiliation(s)
- Corey R Landry
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, United States.
| | - Mighten C Yip
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, United States
| | - Ying Zhou
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, United States
| | - Weibo Niu
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, United States
| | - Yunmiao Wang
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, United States; Department of Biology, Emory University, United States
| | - Bo Yang
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, United States
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, United States; Department of Cell Biology, Emory University School of Medicine, United States
| | - Craig R Forest
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, United States; George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, United States
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32
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Liu JTC, Glaser AK, Poudel C, Vaughan JC. Nondestructive 3D Pathology with Light-Sheet Fluorescence Microscopy for Translational Research and Clinical Assays. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:231-252. [PMID: 36854208 DOI: 10.1146/annurev-anchem-091222-092734] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In recent years, there has been a revived appreciation for the importance of spatial context and morphological phenotypes for both understanding disease progression and guiding treatment decisions. Compared with conventional 2D histopathology, which is the current gold standard of medical diagnostics, nondestructive 3D pathology offers researchers and clinicians the ability to visualize orders of magnitude more tissue within their natural volumetric context. This has been enabled by rapid advances in tissue-preparation methods, high-throughput 3D microscopy instrumentation, and computational tools for processing these massive feature-rich data sets. Here, we provide a brief overview of many of these technical advances along with remaining challenges to be overcome. We also speculate on the future of 3D pathology as applied in translational investigations, preclinical drug development, and clinical decision-support assays.
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Affiliation(s)
- Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA;
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA;
- Allen Institute for Neural Dynamics, Seattle, Washington, USA
| | - Chetan Poudel
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA
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33
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Amin ND, Kelley KW, Hao J, Miura Y, Narazaki G, Li T, McQueen P, Kulkarni S, Pavlov S, Paşca SP. Generating human neural diversity with a multiplexed morphogen screen in organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.541819. [PMID: 37398073 PMCID: PMC10312596 DOI: 10.1101/2023.05.31.541819] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Morphogens choreograph the generation of remarkable cellular diversity in the developing nervous system. Differentiation of stem cells toward particular neural cell fates in vitro often relies upon combinatorial modulation of these signaling pathways. However, the lack of a systematic approach to understand morphogen-directed differentiation has precluded the generation of many neural cell populations, and knowledge of the general principles of regional specification remain in-complete. Here, we developed an arrayed screen of 14 morphogen modulators in human neural organoids cultured for over 70 days. Leveraging advances in multiplexed RNA sequencing technology and annotated single cell references of the human fetal brain we discovered that this screening approach generated considerable regional and cell type diversity across the neural axis. By deconvoluting morphogen-cell type relationships, we extracted design principles of brain region specification, including critical morphogen timing windows and combinatorics yielding an array of neurons with distinct neuro-transmitter identities. Tuning GABAergic neural subtype diversity unexpectedly led to the derivation of primate-specific interneurons. Taken together, this serves as a platform towards an in vitro morphogen atlas of human neural cell differentiation that will bring insights into human development, evolution, and disease.
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Medrano M, Allaoui W, Van Bulck M, Thys S, Makrini-Maleville L, Seuntjens E, De Vos WH, Valjent E, Gaszner B, Van Eeckhaut A, Smolders I, De Bundel D. Neuroanatomical characterization of the Nmu-Cre knock-in mice reveals an interconnected network of unique neuropeptidergic cells. Open Biol 2023; 13:220353. [PMID: 37311538 DOI: 10.1098/rsob.220353] [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: 11/30/2022] [Accepted: 05/10/2023] [Indexed: 06/15/2023] Open
Abstract
Neuromedin U (NMU) is an evolutionary conserved neuropeptide that has been implicated in multiple processes, such as circadian regulation, energy homeostasis, reward processing and stress coping. Although the central expression of NMU has been addressed previously, the lack of specific and sensitive tools has prevented a comprehensive characterization of NMU-expressing neurons in the brain. We have generated a knock-in mouse model constitutively expressing Cre recombinase under the Nmu promoter. We have validated the model using a multi-level approach based on quantitative reverse-transcription polymerase chain reactions, in situ hybridization, a reporter mouse line and an adenoviral vector driving Cre-dependent expression of a fluorescent protein. Using the Nmu-Cre mouse, we performed a complete characterization of NMU expression in adult mouse brain, unveiling a potential midline NMU modulatory circuit with the ventromedial hypothalamic nucleus (VMH) as a key node. Moreover, immunohistochemical analysis suggested that NMU neurons in the VMH mainly constitute a unique population of hypothalamic cells. Taken together, our results suggest that Cre expression in the Nmu-Cre mouse model largely reflects NMU expression in the adult mouse brain, without altering endogenous NMU expression. Thus, the Nmu-Cre mouse model is a powerful and sensitive tool to explore the role of NMU neurons in mice.
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Affiliation(s)
- Mireia Medrano
- Center for Neurosciences, Department of Pharmaceutical Chemistry, Drug Analysis and Drug Information, Research Group Experimental Pharmacology, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Wissal Allaoui
- Center for Neurosciences, Department of Pharmaceutical Chemistry, Drug Analysis and Drug Information, Research Group Experimental Pharmacology, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Mathias Van Bulck
- Laboratory of Medical and Molecular Oncology, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Sofie Thys
- Department of Veterinary Sciences, Laboratory of Cell Biology and Histology and Antwerp Centre for Advanced Microscopy (ACAM), University of Antwerp, 2610 Antwerp, Belgium
| | | | - Eve Seuntjens
- Department of Biology, Laboratory of Developmental Neurobiology, KU Leuven, 3000 Leuven, Belgium
| | - Winnok H De Vos
- Department of Veterinary Sciences, Laboratory of Cell Biology and Histology and Antwerp Centre for Advanced Microscopy (ACAM), University of Antwerp, 2610 Antwerp, Belgium
- μNEURO Research Centre of Excellence, University of Antwerp, 2610 Antwerp, Belgium
- Antwerp Centre for Advanced Microscopy (ACAM), 2610 Wilrijk, Belgium
| | - Emmanuel Valjent
- IGF, Université de Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | - Bálazs Gaszner
- Medical School, Research Group for Mood Disorders, Department of Anatomy and Centre for Neuroscience, University of Pécs, 7624 Pécs, Hungary
| | - Ann Van Eeckhaut
- Center for Neurosciences, Department of Pharmaceutical Chemistry, Drug Analysis and Drug Information, Research Group Experimental Pharmacology, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Ilse Smolders
- Center for Neurosciences, Department of Pharmaceutical Chemistry, Drug Analysis and Drug Information, Research Group Experimental Pharmacology, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Dimitri De Bundel
- Center for Neurosciences, Department of Pharmaceutical Chemistry, Drug Analysis and Drug Information, Research Group Experimental Pharmacology, Vrije Universiteit Brussel, 1090 Brussels, Belgium
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35
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Kasaragod DK, Aizawa H. Deep ultraviolet fluorescence microscopy of three-dimensional structures in the mouse brain. Sci Rep 2023; 13:8553. [PMID: 37237102 DOI: 10.1038/s41598-023-35650-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/22/2023] [Indexed: 05/28/2023] Open
Abstract
Three-dimensional (3D) imaging at cellular resolution improves our understanding of the brain architecture and is crucial for structural and functional integration as well as for the understanding of normal and pathological conditions in the brain. We developed a wide-field fluorescent microscope for 3D imaging of the brain structures using deep ultraviolet (DUV) light. This microscope allowed fluorescence imaging with optical sectioning due to the large absorption at the surface of the tissue and hence low tissue penetration of DUV light. Multiple channels of fluorophore signals were detected using single or a combination of dyes emitting fluorescence in the visible range of spectrum upon DUV excitation. Combination of this DUV microscope with microcontroller-based motorized stage enabled wide-field imaging of a coronal section of the cerebral hemisphere in mouse for deciphering cytoarchitecture of each substructure in detail. We extended this by integrating vibrating microtome which allowed serial block-face imaging of the brain structure such as the habenula in mouse. Acquired images were with resolution high enough for quantification of the cell numbers and density in the mouse habenula. Upon block-face imaging of the tissues covering entire extent of the cerebral hemisphere of the mouse brain, acquired data were registered and segmented for quantification of cell number in each brain regions. Results in the current analysis indicated that this novel microscope could be a convenient tool for large-scale 3D analysis of the brain in mice.
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Affiliation(s)
- Deepa Kamath Kasaragod
- Department of Neurobiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan.
| | - Hidenori Aizawa
- Department of Neurobiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan.
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36
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Yau CN, Lai HM, Lee K, Kwok AJ, Huang J, Ko H. Principles of deep immunohistochemistry for 3D histology. CELL REPORTS METHODS 2023; 3:100458. [PMID: 37323568 PMCID: PMC10261851 DOI: 10.1016/j.crmeth.2023.100458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Deep immunohistochemistry (IHC) is a nascent field in three-dimensional (3D) histology that seeks to achieve thorough, homogeneous, and specific staining of intact tissues for visualization of microscopic architectures and molecular compositions at large spatial scales. Despite the tremendous potential of deep IHC in revealing molecule-structure-function relationships in biology and establishing diagnostic and prognostic features for pathological samples in clinical practice, the complexities and variations in methodologies may hinder its use by interested users. We provide a unified framework of deep immunostaining techniques by discussing the theoretical considerations of the physicochemical processes involved, summarizing the principles applied in contemporary methods, advocating a standardized benchmarking scheme, and highlighting unaddressed issues and future directions. By providing the essential information to guide investigators in customizing immunolabeling pipelines, we also seek to facilitate the adoption of deep IHC for researchers to address a wide range of research questions.
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Affiliation(s)
- Chun Ngo Yau
- Department of Psychiatry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hei Ming Lai
- Department of Psychiatry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Margaret K.L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Krit Lee
- Department of Psychiatry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Andrew J. Kwok
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Margaret K.L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Junzhe Huang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Margaret K.L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Ho Ko
- Department of Psychiatry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Margaret K.L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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37
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Cho W, Kim S, Park YG. Towards multiplexed immunofluorescence of 3D tissues. Mol Brain 2023; 16:37. [PMID: 37131224 PMCID: PMC10155431 DOI: 10.1186/s13041-023-01027-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/14/2023] [Indexed: 05/04/2023] Open
Abstract
Profiling molecular expression in situ allows the integration of biomolecular and cellular features, enabling an in-depth understanding of biological systems. Multiplexed immunofluorescence methods can visualize tens to hundreds of proteins from individual tissue samples, but their application is usually limited to thin tissue sections. Multiplexed immunofluorescence of thick tissues or intact organs will enable high-throughput profiling of cellular protein expression within 3D tissue architectures (e.g., blood vessels, neural projections, tumors), opening a new dimension in diverse biological research and medical applications. We will review current multiplexed immunofluorescence methods and discuss possible approaches and challenges to achieve 3D multiplexed immunofluorescence.
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Affiliation(s)
- Wonjin Cho
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Sehun Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Young-Gyun Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
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38
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Zoabi S, Andreyanov M, Heinrich R, Ron S, Carmi I, Gutfreund Y, Berlin S. A custom-made AAV1 variant (AAV1-T593K) enables efficient transduction of Japanese quail neurons in vitro and in vivo. Commun Biol 2023; 6:337. [PMID: 36977781 PMCID: PMC10050006 DOI: 10.1038/s42003-023-04712-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
The widespread use of rodents in neuroscience has prompted the development of optimized viral variants for transduction of brain cells, in vivo. However, many of the viruses developed are less efficient in other model organisms, with birds being among the most resistant to transduction by current viral tools. Resultantly, the use of genetically-encoded tools and methods in avian species is markedly lower than in rodents; likely holding the field back. We sought to bridge this gap by developing custom viruses towards the transduction of brain cells of the Japanese quail. We first develop a protocol for culturing primary neurons and glia from quail embryos, followed by characterization of cultures via immunostaining, single cell mRNA sequencing, patch clamp electrophysiology and calcium imaging. We then leveraged the cultures for the rapid screening of various viruses, only to find that all yielded poor to no infection of cells in vitro. However, few infected neurons were obtained by AAV1 and AAV2. Scrutiny of the sequence of the AAV receptor found in quails led us to rationally design a custom-made AAV variant (AAV1-T593K; AAV1*) that exhibits improved transduction efficiencies in vitro and in vivo (14- and five-fold, respectively). Together, we present unique culturing method, transcriptomic profiles of quail's brain cells and a custom-tailored AAV1 for transduction of quail neurons in vitro and in vivo.
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Affiliation(s)
- Shaden Zoabi
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Michael Andreyanov
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Ronit Heinrich
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Shaked Ron
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Ido Carmi
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Yoram Gutfreund
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Shai Berlin
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel.
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39
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Wang N, Wang X, Yan T, Xie H, Wang L, Ren F, Chen D, Zhang D, Zeng Q, Zhu S, Chen X. Label-free structural and functional volumetric imaging by dual-modality optical-Raman projection tomography. SCIENCE ADVANCES 2023; 9:eadf3504. [PMID: 36961894 PMCID: PMC10038343 DOI: 10.1126/sciadv.adf3504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Mesoscale volumetric imaging is of great importance for the study of bio-organisms. Among others, optical projection tomography provides unprecedented structural details of specimens, but it requires fluorescence label for chemical targeting. Raman spectroscopic imaging is able to identify chemical components in a label-free manner but lacks microstructure. Here, we present a dual-modality optical-Raman projection tomography (ORPT) technology, which enables label-free three-dimensional imaging of microstructures and components of millimeter-sized samples with a micron-level spatial resolution on the same device. We validate the feasibility of our ORPT system using images of polystyrene beads in a volume, followed by detecting biomolecules of zebrafish and Arabidopsis, demonstrating that fused three-dimensional images of the microstructure and molecular components of bio-samples could be achieved. Last, we observe the fat body of Drosophila melanogaster at different developmental stages. Our proposed technology enables bimodal label-free volumetric imaging of the structure and function of biomolecules in a large sample.
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Affiliation(s)
- Nan Wang
- Biomedical Photonics and Molecular Imaging Laboratory, School of Life Science and Technology, Xidian University, and Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, Xi’an, Shaanxi 710126, China
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xi’an, Shaanxi 710126, China
| | - Xinyu Wang
- Biomedical Photonics and Molecular Imaging Laboratory, School of Life Science and Technology, Xidian University, and Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, Xi’an, Shaanxi 710126, China
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xi’an, Shaanxi 710126, China
| | - Tianyu Yan
- Biomedical Photonics and Molecular Imaging Laboratory, School of Life Science and Technology, Xidian University, and Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, Xi’an, Shaanxi 710126, China
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xi’an, Shaanxi 710126, China
| | - Hui Xie
- Biomedical Photonics and Molecular Imaging Laboratory, School of Life Science and Technology, Xidian University, and Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, Xi’an, Shaanxi 710126, China
| | - Lin Wang
- School of Computer Science and Engineering, Xi’an University of Technology, Xi’an, Shaanxi 710048, China
| | - Feng Ren
- Biomedical Photonics and Molecular Imaging Laboratory, School of Life Science and Technology, Xidian University, and Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, Xi’an, Shaanxi 710126, China
| | - Dan Chen
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xi’an, Shaanxi 710126, China
| | - Dongjie Zhang
- Biomedical Photonics and Molecular Imaging Laboratory, School of Life Science and Technology, Xidian University, and Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, Xi’an, Shaanxi 710126, China
| | - Qi Zeng
- Biomedical Photonics and Molecular Imaging Laboratory, School of Life Science and Technology, Xidian University, and Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, Xi’an, Shaanxi 710126, China
| | - Shouping Zhu
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xi’an, Shaanxi 710126, China
- International Joint Research Center for Advanced Medical Imaging and Intelligent Diagnosis and Treatment, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710126, China
| | - Xueli Chen
- Biomedical Photonics and Molecular Imaging Laboratory, School of Life Science and Technology, Xidian University, and Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, Xi’an, Shaanxi 710126, China
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xi’an, Shaanxi 710126, China
- International Joint Research Center for Advanced Medical Imaging and Intelligent Diagnosis and Treatment, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710126, China
- Innovation Center for Advanced Medical Imaging and Intelligent Medicine, Guangzhou Institute of Technology, Xidian University, Guangzhou, Guangdong 51055, China
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40
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Wu P, Asada H, Hakamada M, Mabuchi M. Bioengineering of High Cell Density Tissues with Hierarchical Vascular Networks for Ex Vivo Whole Organs. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2209149. [PMID: 36545785 DOI: 10.1002/adma.202209149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/25/2022] [Indexed: 06/17/2023]
Abstract
The development of tissue-like structures such as cell sheets, spheroids, and organoids has contributed to progress in regenerative medicine. Simultaneous achievement of scale up and high cell density of these tissues is challenging because sufficient oxygen cannot be supplied to the inside of large, high cell density tissues. Here, in vitro fabrication of vessels to supply oxygen to the inside of millimeter-sized scaffold-free tissues whose cell density is ≈200 million cells mL-1 , corresponding to those of native tissues, is shown. Hierarchical vascular networks by anastomosis of capillaries and a large vessel are essential for oxygen supply, whereas a large vessel or capillary networks alone make negligible contributions to the supply. The hierarchical vascular networks are formed by a top-down approach, which offers a new option for ex vivo whole organs without decellularization and 3D-bioprinting.
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Affiliation(s)
- Peizheng Wu
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, Kyoto, 606-8501, Japan
| | - Hiroki Asada
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, Kyoto, 606-8501, Japan
| | - Masataka Hakamada
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, Kyoto, 606-8501, Japan
| | - Mamoru Mabuchi
- Graduate School of Energy Science, Kyoto University, Yoshidahonmachi, Sakyo, Kyoto, 606-8501, Japan
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41
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Experience-dependent functional plasticity and visual response selectivity of surviving subplate neurons in the mouse visual cortex. Proc Natl Acad Sci U S A 2023; 120:e2217011120. [PMID: 36812195 PMCID: PMC9992851 DOI: 10.1073/pnas.2217011120] [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: 02/24/2023] Open
Abstract
Subplate neurons are early-born cortical neurons that transiently form neural circuits during perinatal development and guide cortical maturation. Thereafter, most subplate neurons undergo cell death, while some survive and renew their target areas for synaptic connections. However, the functional properties of the surviving subplate neurons remain largely unknown. This study aimed to characterize the visual responses and experience-dependent functional plasticity of layer 6b (L6b) neurons, the remnants of subplate neurons, in the primary visual cortex (V1). Two-photon Ca2+ imaging was performed in V1 of awake juvenile mice. L6b neurons showed broader tunings for orientation, direction, and spatial frequency than did layer 2/3 (L2/3) and L6a neurons. In addition, L6b neurons showed lower matching of preferred orientation between the left and right eyes compared with other layers. Post hoc 3D immunohistochemistry confirmed that the majority of recorded L6b neurons expressed connective tissue growth factor (CTGF), a subplate neuron marker. Moreover, chronic two-photon imaging showed that L6b neurons exhibited ocular dominance (OD) plasticity by monocular deprivation during critical periods. The OD shift to the open eye depended on the response strength to the stimulation of the eye to be deprived before starting monocular deprivation. There were no significant differences in visual response selectivity prior to monocular deprivation between the OD changed and unchanged neuron groups, suggesting that OD plasticity can occur in L6b neurons showing any response features. In conclusion, our results provide strong evidence that surviving subplate neurons exhibit sensory responses and experience-dependent plasticity at a relatively late stage of cortical development.
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42
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Efficient 3D light-sheet imaging of very large-scale optically cleared human brain and prostate tissue samples. Commun Biol 2023; 6:170. [PMID: 36781939 PMCID: PMC9925784 DOI: 10.1038/s42003-023-04536-4] [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: 07/26/2022] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
The ability to image human tissue samples in 3D, with both cellular resolution and a large field of view (FOV), can improve fundamental and clinical investigations. Here, we demonstrate the feasibility of light-sheet imaging of ~5 cm3 sized formalin fixed human brain and up to ~7 cm3 sized formalin fixed paraffin embedded (FFPE) prostate cancer samples, processed with the FFPE-MASH protocol. We present a light-sheet microscopy prototype, the cleared-tissue dual view Selective Plane Illumination Microscope (ct-dSPIM), capable of fast 3D high-resolution acquisitions of cm3 scale cleared tissue. We used mosaic scans for fast 3D overviews of entire tissue samples or higher resolution overviews of large ROIs with various speeds: (a) Mosaic 16 (16.4 µm isotropic resolution, ~1.7 h/cm3), (b) Mosaic 4 (4.1 µm isotropic resolution, ~ 5 h/cm3) and (c) Mosaic 0.5 (0.5 µm near isotropic resolution, ~15.8 h/cm3). We could visualise cortical layers and neurons around the border of human brain areas V1&V2, and could demonstrate suitable imaging quality for Gleason score grading in thick prostate cancer samples. We show that ct-dSPIM imaging is an excellent technique to quantitatively assess entire MASH prepared large-scale human tissue samples in 3D, with considerable future clinical potential.
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43
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Chen S, Liu G, Li A, Liu Z, Long B, Yang X, Gong H, Li X. Three-dimensional mapping in multi-samples with large-scale imaging and multiplexed post staining. Commun Biol 2023; 6:148. [PMID: 36737476 PMCID: PMC9898531 DOI: 10.1038/s42003-023-04456-3] [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: 07/22/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Dissection of the anatomical information at the single-cell level is crucial for understanding the organization rule and pathological mechanism of biological tissues. Mapping the whole organ in numerous groups with multiple conditions brings the challenges in imaging and analysis. Here, we describe an approach, named array fluorescent micro-optical sectioning tomography (array-fMOST), to identify the three-dimensional information at single-cell resolution from multi-samples. The pipeline contains array embedding, large-scale imaging, post-imaging staining and data analysis, which could image over 24 mouse brains simultaneously and collect the slices for further analysis. With transgenic mice, we acquired the distribution information of neuropeptide somatostatin neurons during natural aging and compared the changes in the microenvironments by multi-component labeling of serial sections with precise co-registration of serial datasets quantitatively. With viral labeling, we also analyzed the input circuits of the medial prefrontal cortex in the whole brain of Alzheimer's disease and autism model mice. This pipeline is highly scalable to be applied to anatomical alterations screening and identification. It provides new opportunities for combining multi-sample whole-organ imaging and molecular phenotypes identification analysis together. Such integrated high-dimensional information acquisition method may accelerate our understanding of pathogenesis and progression of disease in situ at multiple levels.
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Affiliation(s)
- Siqi Chen
- grid.33199.310000 0004 0368 7223Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074 China
| | - Guangcai Liu
- grid.33199.310000 0004 0368 7223Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074 China
| | - Anan Li
- grid.33199.310000 0004 0368 7223Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074 China ,grid.495419.4Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Sciences, HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, 215125 China
| | - Zhixiang Liu
- grid.33199.310000 0004 0368 7223Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074 China
| | - Ben Long
- grid.428986.90000 0001 0373 6302Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, 570228 China
| | - Xiaoquan Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China. .,Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Sciences, HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, 215125, China.
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China. .,Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Sciences, HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, 215125, China.
| | - Xiangning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China. .,Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Sciences, HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, 215125, China. .,Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, 570228, China.
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Phillips EH, Bindokas VP, Jung D, Teamer J, Kitajewski JK, Solaro RJ, Wolska BM, Lee SSY. Three-dimensional spatial quantitative analysis of cardiac lymphatics in the mouse heart. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526338. [PMID: 36778334 PMCID: PMC9915594 DOI: 10.1101/2023.02.01.526338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Objective 3D microscopy and image data analysis are necessary for studying the morphology of cardiac lymphatic vessels (LyVs) and association with other cell types. We aimed to develop a methodology for 3D multiplexed lightsheet microscopy and highly sensitive and quantitative image analysis to identify pathological remodeling in the 3D morphology of LyVs in young adult mouse hearts with familial hypertrophic cardiomyopathy (HCM). Methods We developed a 3D lightsheet microscopy workflow providing a quick turn-around (as few as 5-6 days), multiplex fluorescence detection, and preservation of LyV structure and epitope markers. Hearts from non-transgenic (NTG) and transgenic (TG) HCM mice were arrested in diastole, retrograde perfused, immunolabeled, optically cleared, and imaged. We built an image processing pipeline to quantify LyV morphological parameters at the chamber and branch levels. Results Chamber-specific pathological alterations of LyVs were identified, but most significantly in the right atrium (RA). TG hearts had a higher volume fraction of ER-TR7 + fibroblasts and reticular fibers. In the RA, we found associations between ER-TR7 + volume fraction and both LyV segment density and median diameter. Conclusions This workflow and study enabled multi-scale analysis of pathological changes in cardiac LyVs of young adult mice, inviting ideas for research on LyVs in cardiac disease.
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Nonaka H, Mino T, Sakamoto S, Oh JH, Watanabe Y, Ishikawa M, Tsushima A, Amaike K, Kiyonaka S, Tamura T, Aricescu AR, Kakegawa W, Miura E, Yuzaki M, Hamachi I. Revisiting PFA-mediated tissue fixation chemistry: FixEL enables trapping of small molecules in the brain to visualize their distribution changes. Chem 2023; 9:523-540. [PMID: 38094901 PMCID: PMC7615374 DOI: 10.1016/j.chempr.2022.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Various small molecules have been used as functional probes for tissue imaging in medical diagnosis and pharmaceutical drugs for disease treatment. The spatial distribution, target selectivity, and diffusion/excretion kinetics of small molecules in structurally complicated specimens are critical for function. However, robust methods for precisely evaluating these parameters in the brain have been limited. Herein, we report a new method termed "fixation-driven chemical cross-linking of exogenous ligands (FixEL)," which traps and images exogenously administered molecules of interest (MOIs) in complex tissues. This method relies on protein-MOI interactions and chemical cross-linking of amine-tethered MOI with paraformaldehyde used for perfusion fixation. FixEL is used to obtain images of the distribution of the small molecules, which addresses selective/nonselective binding to proteins, time-dependent localization changes, and diffusion/retention kinetics of MOIs such as the scaffold of PET tracer derivatives or drug-like small molecules.
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Affiliation(s)
- Hiroshi Nonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - Takeharu Mino
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Jae Hoon Oh
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - Yu Watanabe
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Mamoru Ishikawa
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - Akihiro Tsushima
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Kazuma Amaike
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Shigeki Kiyonaka
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - A. Radu Aricescu
- Division of Structural Biology, University of Oxford, Oxford OX3 7BN, UK
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Wataru Kakegawa
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
- Department of Neurophysiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Eriko Miura
- Department of Neurophysiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Michisuke Yuzaki
- Department of Neurophysiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
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Zwang TJ, Bennett RE, Lysandrou M, Woost B, Zhang A, Lieber CM, Richardson DS, Hyman BT. Tissue libraries enable rapid determination of conditions that preserve antibody labeling in cleared mouse and human tissue. eLife 2023; 12:e84112. [PMID: 36656755 PMCID: PMC9889093 DOI: 10.7554/elife.84112] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/18/2023] [Indexed: 01/20/2023] Open
Abstract
Difficulty achieving complete, specific, and homogenous staining is a major bottleneck preventing the widespread use of tissue clearing techniques to image large volumes of human tissue. In this manuscript, we describe a procedure to rapidly design immunostaining protocols for antibody labeling of cleared brain tissue. We prepared libraries of 0.5-1.0 mm thick tissue sections that are fixed, pre-treated, and cleared via similar, but different procedures to optimize staining conditions for a panel of antibodies. Results from a library of mouse tissue correlate well with results from a similarly prepared library of human brain tissue, suggesting mouse tissue is an adequate substitute for protocol optimization. These data show that procedural differences do not influence every antibody-antigen pair in the same way, and minor changes can have deleterious effects, therefore, optimization should be conducted for each target. The approach outlined here will help guide researchers to successfully label a variety of targets, thus removing a major hurdle to accessing the rich 3D information available in large, cleared human tissue volumes.
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Affiliation(s)
- Theodore J Zwang
- Department of Neurology, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Harvard Medical SchoolBostonUnited States
- Massachusetts Alzheimer’s Disease Research CenterCharlestownUnited States
| | - Rachel E Bennett
- Department of Neurology, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Harvard Medical SchoolBostonUnited States
- Massachusetts Alzheimer’s Disease Research CenterCharlestownUnited States
| | - Maria Lysandrou
- Department of Neurology, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Benjamin Woost
- Department of Neurology, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Anqi Zhang
- Department of Chemical Engineering, Stanford UniversityStanfordUnited States
| | - Charles M Lieber
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Douglas S Richardson
- Department of Molecular and Cellular Biology and Harvard Center for Biological Imaging, Harvard UniversityCambridgeUnited States
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Harvard Medical SchoolBostonUnited States
- Massachusetts Alzheimer’s Disease Research CenterCharlestownUnited States
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Murphy RJ, Gunasingh G, Haass NK, Simpson MJ. Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability. PLoS Comput Biol 2023; 19:e1010833. [PMID: 36634128 PMCID: PMC9876349 DOI: 10.1371/journal.pcbi.1010833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/25/2023] [Accepted: 12/21/2022] [Indexed: 01/13/2023] Open
Abstract
Tumours are subject to external environmental variability. However, in vitro tumour spheroid experiments, used to understand cancer progression and develop cancer therapies, have been routinely performed for the past fifty years in constant external environments. Furthermore, spheroids are typically grown in ambient atmospheric oxygen (normoxia), whereas most in vivo tumours exist in hypoxic environments. Therefore, there are clear discrepancies between in vitro and in vivo conditions. We explore these discrepancies by combining tools from experimental biology, mathematical modelling, and statistical uncertainty quantification. Focusing on oxygen variability to develop our framework, we reveal key biological mechanisms governing tumour spheroid growth. Growing spheroids in time-dependent conditions, we identify and quantify novel biological adaptation mechanisms, including unexpected necrotic core removal, and transient reversal of the tumour spheroid growth phases.
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Affiliation(s)
- Ryan J. Murphy
- Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- * E-mail:
| | - Gency Gunasingh
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Nikolas K. Haass
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Matthew J. Simpson
- Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
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Unnersjö-Jess D. Quantitative Imaging of Podocyte Foot Processes in the Kidney Using Confocal and STED Microscopy. Methods Mol Biol 2023; 2664:185-199. [PMID: 37423991 DOI: 10.1007/978-1-0716-3179-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Morphological alterations to the kidney filter, particularly to podocyte foot processes, are seen in most types of glomerular diseases. Due to the nanoscale dimensions of the filter, visualization of such alterations has historically relied on electron microscopy. However, with recent technical development, it is now possible to also visualize podocyte foot processes, as well as other parts of the kidney filtration barrier, with light microscopy. With developments both in sample preparation, imaging, and image analysis, these new tools are becoming increasingly applied in kidney research, due to their demonstrated quantitative potential. We here present an overview of these protocols that can be applied to samples that have been fixed and stored using most standard procedures used today (i.e., PFA fixed, fresh frozen, formalin-fixed and paraffin-embedded (FFPE)). We additionally introduce tools for quantitative image analysis of foot process morphology and foot process effacement.
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Affiliation(s)
- David Unnersjö-Jess
- Department II of Internal Medicine and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- MedTechLabs, Karolinska University Hospital, Solna, Sweden.
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Balcaen T, Piens C, Mwema A, Chourrout M, Vandebroek L, Des Rieux A, Chauveau F, De Borggraeve WM, Hoffmann D, Kerckhofs G. Revealing the three-dimensional murine brain microstructure by contrast-enhanced computed tomography. Front Neurosci 2023; 17:1141615. [PMID: 37034159 PMCID: PMC10076597 DOI: 10.3389/fnins.2023.1141615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
To improve our understanding of the brain microstructure, high-resolution 3D imaging is used to complement classical 2D histological assessment techniques. X-ray computed tomography allows high-resolution 3D imaging, but requires methods for enhancing contrast of soft tissues. Applying contrast-enhancing staining agents (CESAs) ameliorates the X-ray attenuating properties of soft tissue constituents and is referred to as contrast-enhanced computed tomography (CECT). Despite the large number of chemical compounds that have successfully been applied as CESAs for imaging brain, they are often toxic for the researcher, destructive for the tissue and without proper characterization of affinity mechanisms. We evaluated two sets of chemically related CESAs (organic, iodinated: Hexabrix and CA4+ and inorganic polyoxometalates: 1:2 hafnium-substituted Wells-Dawson phosphotungstate and Preyssler anion), for CECT imaging of healthy murine hemispheres. We then selected the CESA (Hexabrix) that provided the highest contrast between gray and white matter and applied it to a cuprizone-induced demyelination model. Differences in the penetration rate, effect on tissue integrity and affinity for tissue constituents have been observed for the evaluated CESAs. Cuprizone-induced demyelination could be visualized and quantified after Hexabrix staining. Four new non-toxic and non-destructive CESAs to the field of brain CECT imaging were introduced. The added value of CECT was shown by successfully applying it to a cuprizone-induced demyelination model. This research will prove to be crucial for further development of CESAs for ex vivo brain CECT and 3D histopathology.
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Affiliation(s)
- Tim Balcaen
- MolDesignS, Sustainable Chemistry for Metals and Molecules, Department of Chemistry, KU Leuven, Leuven, Belgium
- ContrasT Team, Institute of Mechanics, Materials and Civil Engineering, Mechatronic, Electrical Energy and Dynamic Systems, UCLouvain, Louvain-la-Neuve, Belgium
- Pole of Morphology, Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium
| | - Catherine Piens
- ContrasT Team, Institute of Mechanics, Materials and Civil Engineering, Mechatronic, Electrical Energy and Dynamic Systems, UCLouvain, Louvain-la-Neuve, Belgium
| | - Ariane Mwema
- Advanced Drug Delivery and Biomaterials, UCLouvain, Brussels, Belgium
- Bioanalysis and Pharmacology of Bioactive Lipids, UCLouvain, Brussels, Belgium
| | - Matthieu Chourrout
- Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre de Recherche en Neurosciences de Lyon U1028 UMR 5292, Bron, France
| | - Laurens Vandebroek
- Laboratory of Biomolecular Modelling and Design (LBMD), Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Anne Des Rieux
- Advanced Drug Delivery and Biomaterials, UCLouvain, Brussels, Belgium
| | - Fabien Chauveau
- Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre de Recherche en Neurosciences de Lyon U1028 UMR 5292, Bron, France
| | - Wim M. De Borggraeve
- MolDesignS, Sustainable Chemistry for Metals and Molecules, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Delia Hoffmann
- Pole of Morphology, Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium
- Skeletal Biology and Engineering Research Center, KU Leuven, Leuven, Belgium
| | - Greet Kerckhofs
- ContrasT Team, Institute of Mechanics, Materials and Civil Engineering, Mechatronic, Electrical Energy and Dynamic Systems, UCLouvain, Louvain-la-Neuve, Belgium
- Pole of Morphology, Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium
- Department Materials Engineering, KU Leuven, Leuven, Belgium
- *Correspondence: Greet Kerckhofs,
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50
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Three-dimensional visualization of human brain tumors using the CUBIC technique. Brain Tumor Pathol 2023; 40:4-14. [PMID: 36370248 DOI: 10.1007/s10014-022-00445-2] [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: 06/27/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022]
Abstract
Application of tissue clearing techniques on human brain tumors is still limited. This study was to investigate the application of CUBIC on 3D pathological studies of human brain tumors. Brain tumor specimens derived from 21 patients were cleared with CUBIC. Immunostaining was conducted on cleared specimens to label astrocytes, microglia and microvessels, respectively. All tumor specimens achieved transparency after clearing. Immunostaining and CUBIC are well compatible in a variety of human brain tumors. Spatial morphologies of microvessels, astrocytes and microglia of tumors were clearly visualized in 3D, and their 3D morphological parameters were easily quantified. By comparing the quantitative morphological parameters of microvessels among brain tumors of different malignancy, we found that mean vascular diameter was positively correlated with tumor malignancy. Our study demonstrates that CUBIC can be successfully applied to 3D pathological studies of various human brain tumors, and 3D studies of human brain tumors hold great promise in helping us better understand brain tumor pathology in the future.
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