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Jevans B, Cooper F, Fatieieva Y, Gogolou A, Kang YN, Restuadi R, Moulding D, Vanden Berghe P, Adameyko I, Thapar N, Andrews PW, De Coppi P, Tsakiridis A, McCann CJ. Human enteric nervous system progenitor transplantation improves functional responses in Hirschsprung disease patient-derived tissue. Gut 2024; 73:1441-1453. [PMID: 38816188 DOI: 10.1136/gutjnl-2023-331532] [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: 11/14/2023] [Accepted: 05/07/2024] [Indexed: 06/01/2024]
Abstract
OBJECTIVE Hirschsprung disease (HSCR) is a severe congenital disorder affecting 1:5000 live births. HSCR results from the failure of enteric nervous system (ENS) progenitors to fully colonise the gastrointestinal tract during embryonic development. This leads to aganglionosis in the distal bowel, resulting in disrupted motor activity and impaired peristalsis. Currently, the only viable treatment option is surgical resection of the aganglionic bowel. However, patients frequently suffer debilitating, lifelong symptoms, with multiple surgical procedures often necessary. Hence, alternative treatment options are crucial. An attractive strategy involves the transplantation of ENS progenitors generated from human pluripotent stem cells (hPSCs). DESIGN ENS progenitors were generated from hPSCs using an accelerated protocol and characterised, in detail, through a combination of single-cell RNA sequencing, protein expression analysis and calcium imaging. We tested ENS progenitors' capacity to integrate and affect functional responses in HSCR colon, after ex vivo transplantation to organotypically cultured patient-derived colonic tissue, using organ bath contractility. RESULTS We found that our protocol consistently gives rise to high yields of a cell population exhibiting transcriptional and functional hallmarks of early ENS progenitors. Following transplantation, hPSC-derived ENS progenitors integrate, migrate and form neurons/glia within explanted human HSCR colon samples. Importantly, the transplanted HSCR tissue displayed significantly increased basal contractile activity and increased responses to electrical stimulation compared with control tissue. CONCLUSION Our findings demonstrate, for the first time, the potential of hPSC-derived ENS progenitors to repopulate and increase functional responses in human HSCR patient colonic tissue.
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Affiliation(s)
- Benjamin Jevans
- Stem Cells and Regenerative Medicine, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - Fay Cooper
- School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Yuliia Fatieieva
- Department of Neuroimmunology, Centre for Brain Research, Medical University of Vienna, Wien, Austria
| | - Antigoni Gogolou
- School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Yi-Ning Kang
- Laboratory for Enteric NeuroScience (LENS), Translational Research Centre for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Restuadi Restuadi
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - Dale Moulding
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - Pieter Vanden Berghe
- Laboratory for Enteric NeuroScience (LENS), Translational Research Centre for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium
- Cell and Tissue Imaging Cluster (CIC), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Igor Adameyko
- Department of Neuroimmunology, Centre for Brain Research, Medical University of Vienna, Wien, Austria
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Nikhil Thapar
- Stem Cells and Regenerative Medicine, UCL GOS Institute of Child Health, London, UK
- Gastroenterology, Hepatology and Liver Transplant, Queensland Children's Hospital UQ Faculty, South Brisbane, Queensland, Australia
| | - Peter W Andrews
- School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Paolo De Coppi
- Stem Cells and Regenerative Medicine, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
- Specialist Neonatal and Paediatric Surgery Unit, Great Ormond Street Hospital, London, UK
| | - Anestis Tsakiridis
- School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Conor J McCann
- Stem Cells and Regenerative Medicine, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
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Park JM, Choi SH, Lee ES, Gum SI, Hong S, Kim DS, Han MH, Lee SH, Oh JW. High-Speed Clearing and High-Resolution Staining for Analysis of Various Markers for Neurons and Vessels. Tissue Eng Regen Med 2024:10.1007/s13770-024-00658-w. [PMID: 38955906 DOI: 10.1007/s13770-024-00658-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Tissue clearing enables deep imaging in various tissues by increasing the transparency of tissues, but there were limitations of immunostaining of the large-volume tissues such as the whole brain. METHODS Here, we cleared and immune-stained whole mouse brain tissues using a novel clearing technique termed high-speed clearing and high-resolution staining (HCHS). We observed neural structures within the cleared brains using both a confocal microscope and a light-sheet fluorescence microscope (LSFM). The reconstructed 3D images were analyzed using a computational reconstruction algorithm. RESULTS Various neural structures were well observed in three-dimensional (3D) images of the cleared brains from Gad-green fluorescent protein (GFP) mice and Thy 1-yellow fluorescent protein (YFP) mice. The intrinsic fluorescence signals of both transgenic mice were preserved after HCHS. In addition, large-scale 3D imaging of brains, immune-stained by the HCHS method using a mild detergent-based solution, allowed for the global topological analysis of several neuronal markers such as c-Fos, neuronal nuclear protein (NeuN), Microtubule-associated protein 2 (Map2), Tuj1, glial fibrillary acidic protein (GFAP), and tyrosine hydroxylase (TH) in various anatomical regions in the whole mouse brain tissues. Finally, through comparisons with various existing tissue clearing methodologies such as CUBIC, Visikol, and 3DISCO, it was confirmed that the HCHS methodology results in relatively less tissue deformation and higher fluorescence retention. CONCLUSION In conclusion, the development of 3D imaging based on novel tissue-clearing techniques (HCHS) will enable detailed spatial analysis of neural and vascular networks present within the brain.
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Affiliation(s)
- Jung Min Park
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Anatomy, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
- BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Seock Hwan Choi
- Department of Urology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
- Bio-Medical Research Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Eun-Shil Lee
- Institute of Biomedical Engineering Research, Kyungpook National University, Daegu, Republic of Korea
| | | | - Sungkuk Hong
- Department of Anatomy, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
- BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
- Binaree, Inc., Daegu, Republic of Korea
| | - Dong Sun Kim
- Department of Anatomy, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
- BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Man-Hoon Han
- Bio-Medical Research Institute, Kyungpook National University, Daegu, Republic of Korea
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Soung-Hoon Lee
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Ji Won Oh
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea.
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3
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André M, Dinvaut S, Castellani V, Falk J. 3D exploration of gene expression in chicken embryos through combined RNA fluorescence in situ hybridization, immunofluorescence, and clearing. BMC Biol 2024; 22:131. [PMID: 38831263 PMCID: PMC11149291 DOI: 10.1186/s12915-024-01922-0] [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: 07/06/2023] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Fine characterization of gene expression patterns is crucial to understand many aspects of embryonic development. The chicken embryo is a well-established and valuable animal model for developmental biology. The period spanning from the third to sixth embryonic days (E3 to E6) is critical for many organ developments. Hybridization chain reaction RNA fluorescent in situ hybridization (HCR RNA-FISH) enables multiplex RNA detection in thick samples including embryos of various animal models. However, its use is limited by tissue opacity. RESULTS We optimized HCR RNA-FISH protocol to efficiently label RNAs in whole mount chicken embryos from E3.5 to E5.5 and adapted it to ethyl cinnamate (ECi) tissue clearing. We show that light sheet imaging of HCR RNA-FISH after ECi clearing allows RNA expression analysis within embryonic tissues with good sensitivity and spatial resolution. Finally, whole mount immunofluorescence can be performed after HCR RNA-FISH enabling as exemplified to assay complex spatial relationships between axons and their environment or to monitor GFP electroporated neurons. CONCLUSIONS We could extend the use of HCR RNA-FISH to older chick embryos by optimizing HCR RNA-FISH and combining it with tissue clearing and 3D imaging. The integration of immunostaining makes possible to combine gene expression with classical cell markers, to correlate expressions with morphological differentiation and to depict gene expressions in gain or loss of function contexts. Altogether, this combined procedure further extends the potential of HCR RNA-FISH technique for chicken embryology.
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Affiliation(s)
- Maëlys André
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France.
| | - Sarah Dinvaut
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France
| | - Valérie Castellani
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France
| | - Julien Falk
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France.
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He C, Yuan Y, Gong C, Wang X, Lyu G. Applications of Tissue Clearing in Central and Peripheral Nerves. Neuroscience 2024; 546:104-117. [PMID: 38570062 DOI: 10.1016/j.neuroscience.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
The techniques of tissue clearing have been proposed and applied in anatomical and biomedical research since the 19th century. As we all know, the original study of the nervous system relied on serial ultrathin sections and stereoscopic techniques. The 3D visualization of the nervous system was established by software splicing and reconstruction. With the development of science and technology, microscope equipment had constantly been upgraded. Despite the great progress that has been made in this field, the workload is too complex, and it needs high technical requirements. Abundant mistakes due to manual sections were inescapable and structural integrity remained questionable. According to the classification of tissue transparency methods, we introduced the latest application of transparency methods in central and peripheral nerve research from optical imaging, molecular markers and data analysis. This review summarizes the application of transparent technology in neural pathways. We hope to provide some inspiration for the continuous optimization of tissue clearing methods.
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Affiliation(s)
- Cheng He
- Department of Anatomy, Medical School of Nantong University, Nantong, China
| | - Ye Yuan
- Department of Anatomy, Medical School of Nantong University, Nantong, China
| | - Chuanhui Gong
- Department of Anatomy, Medical School of Nantong University, Nantong, China
| | - Xueying Wang
- Medical School of Nantong University, Nantong, China
| | - Guangming Lyu
- Department of Anatomy, Medical School of Nantong University, Nantong, China; Department of Anatomy, Institute of Neurobiology, Jiangsu Key Laboratory of Neuroregeneration, Medical School of Nantong University, Nantong, China.
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5
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Yi Y, Li Y, Zhang S, Men Y, Wang Y, Jing D, Ding J, Zhu Q, Chen Z, Chen X, Li JL, Wang Y, Wang J, Peng H, Zhang L, Luo W, Feng JQ, He Y, Ge WP, Zhao H. Mapping of individual sensory nerve axons from digits to spinal cord with the transparent embedding solvent system. Cell Res 2024; 34:124-139. [PMID: 38168640 PMCID: PMC10837210 DOI: 10.1038/s41422-023-00867-3] [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: 02/22/2023] [Accepted: 08/07/2023] [Indexed: 01/05/2024] Open
Abstract
Achieving uniform optical resolution for a large tissue sample is a major challenge for deep imaging. For conventional tissue clearing methods, loss of resolution and quality in deep regions is inevitable due to limited transparency. Here we describe the Transparent Embedding Solvent System (TESOS) method, which combines tissue clearing, transparent embedding, sectioning and block-face imaging. We used TESOS to acquire volumetric images of uniform resolution for an adult mouse whole-body sample. The TESOS method is highly versatile and can be combined with different microscopy systems to achieve uniformly high resolution. With a light sheet microscope, we imaged the whole body of an adult mouse, including skin, at a uniform 0.8 × 0.8 × 3.5 μm3 voxel resolution within 120 h. With a confocal microscope and a 40×/1.3 numerical aperture objective, we achieved a uniform sub-micron resolution in the whole sample to reveal a complete projection of individual nerve axons within the central or peripheral nervous system. Furthermore, TESOS allowed the first mesoscale connectome mapping of individual sensory neuron axons spanning 5 cm from adult mouse digits to the spinal cord at a uniform sub-micron resolution.
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Affiliation(s)
- Yating Yi
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Chinese Institute for Brain Research, Beijing, China
| | - Youqi Li
- Chinese Institute for Brain Research, Beijing, China
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Shiwen Zhang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yi Men
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yuhong Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Dian Jing
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology, Shanghai, China
| | - Jiayi Ding
- Chinese Institute for Brain Research, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Qingjie Zhu
- Chinese Institute for Brain Research, Beijing, China
| | - Zexi Chen
- Chinese Institute for Brain Research, Beijing, China
| | - Xingjun Chen
- Chinese Institute for Brain Research, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jun-Liszt Li
- Chinese Institute for Brain Research, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yilong Wang
- Chinese Institute for Brain Research, Beijing, China
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jun Wang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Hanchuan Peng
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | | | - Jian Q Feng
- Texas A&M University, College of Dentistry, Dallas, TX, USA
| | - Yongwen He
- Qujing Medical College, Qujing, Yunnan, China.
| | - Woo-Ping Ge
- Chinese Institute for Brain Research, Beijing, China.
| | - Hu Zhao
- Chinese Institute for Brain Research, Beijing, China.
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Bakis I, Sun Y, Abd Elmagid L, Feng X, Garibyan M, Yip JK, Yu FZ, Chowdhary S, Fernandez GE, Cao J, McCain ML, Lien CL, Harrison MR. Methods for dynamic and whole volume imaging of the zebrafish heart. Dev Biol 2023; 504:75-85. [PMID: 37708968 PMCID: PMC10841891 DOI: 10.1016/j.ydbio.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/02/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
Tissue development and regeneration are dynamic processes involving complex cell migration and cell-cell interactions. We have developed a protocol for complementary time-lapse and three-dimensional (3D) imaging of tissue for developmental and regeneration studies which we apply here to the zebrafish cardiac vasculature. 3D imaging of fixed specimens is used to first define the subject at high resolution then live imaging captures how it changes dynamically. Hearts from adult and juvenile zebrafish are extracted and cleaned in preparation for the different imaging modalities. For whole-mount 3D confocal imaging, single or multiple hearts with native fluorescence or immuno-labeling are prepared for stabilization or clearing, and then imaged. For live imaging, hearts are placed in a prefabricated fluidic device and set on a temperature-controlled microscope for culture and imaging over several days. This protocol allows complete visualization of morphogenic processes in a 3D context and provides the ability to follow cell behaviors to complement in vivo and fixed tissue studies. This culture and imaging protocol can be applied to different cell and tissue types. Here, we have used it to observe zebrafish coronary vasculature and the migration of coronary endothelial cells during heart regeneration.
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Affiliation(s)
- Isaac Bakis
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA; Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10021, USA
| | - Yuhan Sun
- Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Laila Abd Elmagid
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA; Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10021, USA
| | - Xidi Feng
- Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Mher Garibyan
- Laboratory for Living Systems Engineering, Alfred E. Mann Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Joycelyn K Yip
- Laboratory for Living Systems Engineering, Alfred E. Mann Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Fang Zhou Yu
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA; Department of Emergency Medicine, Nuvance Health, Poughkeepsie, NY, 12601, USA
| | - Sayali Chowdhary
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA; Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10021, USA
| | - Gerardo Esteban Fernandez
- Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Jingli Cao
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA; Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10021, USA
| | - Megan L McCain
- Laboratory for Living Systems Engineering, Alfred E. Mann Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA, 90089, USA; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Ching-Ling Lien
- Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA; Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
| | - Michael Rm Harrison
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA; Department of Cell and Developmental Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10021, USA.
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7
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Delage E, Guilbert T, Yates F. Successful 3D imaging of cleared biological samples with light sheet fluorescence microscopy. J Cell Biol 2023; 222:e202307143. [PMID: 37847528 PMCID: PMC10583220 DOI: 10.1083/jcb.202307143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023] Open
Abstract
In parallel with the development of tissue-clearing methods, over the last decade, light sheet fluorescence microscopy has contributed to major advances in various fields, such as cell and developmental biology and neuroscience. While biologists are increasingly integrating three-dimensional imaging into their research projects, their experience with the technique is not always up to their expectations. In response to a survey of specific challenges associated with sample clearing and labeling, image acquisition, and data analysis, we have critically assessed the recent literature to characterize the difficulties inherent to light sheet fluorescence microscopy applied to cleared biological samples and to propose solutions to overcome them. This review aims to provide biologists interested in light sheet fluorescence microscopy with a primer for the development of their imaging pipeline, from sample preparation to image analysis. Importantly, we believe that issues could be avoided with better anticipation of image analysis requirements, which should be kept in mind while optimizing sample preparation and acquisition parameters.
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Affiliation(s)
- Elise Delage
- CellTechs Laboratory, SupBiotech, Villejuif, France
- Service d’Etude des Prions et des Infections Atypiques, Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives, Université Paris Saclay, Fontenay-aux-Roses, France
| | - Thomas Guilbert
- Institut Cochin, Institut national de la santé et de la recherche médicale (U1016), Centre National de la Recherche Scientifique (UMR 8104), Université de Paris (UMR-S1016), Paris, France
| | - Frank Yates
- CellTechs Laboratory, SupBiotech, Villejuif, France
- Service d’Etude des Prions et des Infections Atypiques, Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives, Université Paris Saclay, Fontenay-aux-Roses, France
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8
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Dennis EJ, Bibawi P, Dhanerawala ZM, Lynch LA, Wang SSH, Brody CD. Princeton RAtlas: A Common Coordinate Framework for Fully cleared, Whole Rattus norvegicus Brains. Bio Protoc 2023; 13:e4854. [PMID: 37900100 PMCID: PMC10603261 DOI: 10.21769/bioprotoc.4854] [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: 04/16/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 10/31/2023] Open
Abstract
Whole-brain clearing and imaging methods are becoming more common in mice but have yet to become standard in rats, at least partially due to inadequate clearing from most available protocols. Here, we build on recent mouse-tissue clearing and light-sheet imaging methods and develop and adapt them to rats. We first used cleared rat brains to create an open-source, 3D rat atlas at 25 μm resolution. We then registered and imported other existing labeled volumes and made all of the code and data available for the community (https://github.com/emilyjanedennis/PRA) to further enable modern, whole-brain neuroscience in the rat. Key features • This protocol adapts iDISCO (Renier et al., 2014) and uDISCO (Pan et al., 2016) tissue-clearing techniques to consistently clear rat brains. • This protocol also decreases the number of working hours per day to fit in an 8 h workday. Graphical overview.
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Affiliation(s)
- Emily Jane Dennis
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, USA
| | - Peter Bibawi
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
- Neurology Department, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Zahra M. Dhanerawala
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
- Washington University School of Medicine, St. Louis, Missouri, USA
| | - Laura A. Lynch
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
| | - Samuel S.-H. Wang
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
| | - Carlos D. Brody
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, USA
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9
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Sánchez-Carbonell M, Jiménez Peinado P, Bayer-Kaufmann C, Hennings JC, Hofmann Y, Schmidt S, Witte OW, Urbach A. Effect of methanol fixation on single-cell RNA sequencing of the murine dentate gyrus. Front Mol Neurosci 2023; 16:1223798. [PMID: 37860083 PMCID: PMC10582346 DOI: 10.3389/fnmol.2023.1223798] [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: 05/16/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) provides a powerful tool to evaluate the transcriptomic landscape and heterogeneity of thousands of cells in parallel. However, complex study designs or the unavailability of in-house instruments require the temporal disconnection between sample preparation and library construction, raising the need for efficient sample preservation methods which are compatible with scRNA-seq downstream analysis. Several studies evaluated the effect of methanol fixation as preservation method, yet none of them deeply assessed its effect on adult primary dissociated brain tissue. Here, we evaluated its effect on murine dentate gyrus (DG) single cell suspensions and on subsequent scRNA-seq downstream analysis by performing SOrting and Robot-assisted Transcriptome SEQuencing (SORT-seq), a partially robotized version of the CEL-seq2 protocol. Our results show that MeOH fixation preserves RNA integrity and has no apparent effects on cDNA library construction. They also suggest that fixation protects from sorting-induced cell stress and increases the proportion of high-quality cells. Despite evidence of mRNA leakage in fixed cells, their relative gene expression levels correlate well with those of fresh cells and fixation does not significantly affect the variance of the dataset. Moreover, it allows the identification of all major DG cell populations, including neural precursors, granule neurons and different glial cell types, with a tendency to preserve more neurons that are underrepresented in fresh samples. Overall, our data show that MeOH fixation is suitable for preserving primary neural cells for subsequent single-cell RNA profiling, helping to overcome challenges arising from complex workflows, improve experimental flexibility and facilitate scientific collaboration.
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Affiliation(s)
| | | | | | | | - Yvonne Hofmann
- Department of Internal Medicine V, Jena University Hospital, Jena, Germany
| | - Silvio Schmidt
- Department of Neurology, Jena University Hospital, Jena, Germany
- Jena Center for Healthy Aging, Jena University Hospital, Jena, Germany
- Brain Imaging Center, Jena University Hospital, Jena, Germany
| | - Otto W. Witte
- Department of Neurology, Jena University Hospital, Jena, Germany
- Jena Center for Healthy Aging, Jena University Hospital, Jena, Germany
- Aging Research Center (ARC) Jena, Jena, Germany
| | - Anja Urbach
- Department of Neurology, Jena University Hospital, Jena, Germany
- Jena Center for Healthy Aging, Jena University Hospital, Jena, Germany
- Aging Research Center (ARC) Jena, Jena, Germany
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10
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Heredia JE, Jung M, Balestrini A, Doerr J, Paler-Martinez A, Mozzarelli A, Riol-Blanco L, Kaminker JS, Ding N. Single-Cell Transcriptomic Analysis Links Nonmyelinating Schwann Cells to Proinflammatory Response in the Lung. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:844-852. [PMID: 37477665 PMCID: PMC10450159 DOI: 10.4049/jimmunol.2200946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/23/2023] [Indexed: 07/22/2023]
Abstract
The lung is a barrier tissue with constant exposure to the inhaled environment. Therefore, innate immunity against particulates and pathogens is of critical importance to maintain tissue homeostasis. Although the lung harbors both myelinating and nonmyelinating Schwann cells (NMSCs), NMSCs represent the most abundant Schwann cell (SC) population in the lung. However, their contribution to lung physiology remains largely unknown. In this study, we used the human glial fibrillary acidic protein promoter driving tdTomato expression in mice to identify SCs in the peripheral nervous system and determine their location within the lung. Single-cell transcriptomic analysis revealed the existence of two NMSC populations (NMSC1 and NMSC2) that may participate in pathogen recognition. We demonstrated that these pulmonary SCs produce chemokines and cytokines upon LPS stimulation using in vitro conditions. Furthermore, we challenged mouse lungs with LPS and found that NMSC1 exhibits an enriched proinflammatory response among all SC subtypes. Collectively, these findings define the molecular profiles of lung SCs and suggest a potential role for NMSCs in lung inflammation.
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Affiliation(s)
- Jose E. Heredia
- Department of Discovery Immunology, Genentech, South San Francisco, CA
| | - Min Jung
- Department of OMNI Bioinformatics, Genentech, South San Francisco, CA
| | | | - Jonas Doerr
- Department of Pathology, Genentech, South San Francisco, CA
| | | | | | | | | | - Ning Ding
- Department of Discovery Immunology, Genentech, South San Francisco, CA
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11
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Ushakov DS, Finke S. Tissue optical clearing and 3D imaging of virus infections. Adv Virus Res 2023; 116:89-121. [PMID: 37524483 DOI: 10.1016/bs.aivir.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Imaging pathogens within 3D environment of biological tissues provides spatial information about their localization and interactions with the host. Technological advances in fluorescence microscopy and 3D image analysis now permit visualization and quantification of pathogens directly in large tissue volumes and in great detail. In recent years large volume imaging became an important tool in virology research helping to understand the properties of viruses and the host response to infection. In this chapter we give a review of fluorescence microscopy modalities and tissue optical clearing methods used for large volume tissue imaging. A summary of recent applications for virus research is provided with particular emphasis on studies using light sheet fluorescence microscopy. We describe the challenges and approaches for volumetric image analysis. Practical examples of volumetric imaging implemented in virology laboratories and addressing specialized research questions, such as virus tropism and immune host response are described. We conclude with an overview of the emerging technologies and their potential for virus research.
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Affiliation(s)
- Dmitry S Ushakov
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
| | - Stefan Finke
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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12
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Weiss F, Atlasy N, van Reijmersdal V, Stunnenberg H, Hulsbergen-Veelken C, Friedl P. 3D spheroid culture to examine adaptive therapy response in invading tumor cells. IN VITRO MODELS 2023; 1:463-471. [PMID: 37096022 PMCID: PMC10119213 DOI: 10.1007/s44164-022-00040-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 04/26/2023]
Abstract
3D in vitro culture models of cancer cells in extracellular matrix (ECM) have been developed to investigate drug targeting and resistance or, alternatively, mechanisms of invasion; however, models allowing analysis of shared pathways mediating invasion and therapy resistance are lacking. To evaluate therapy response associated with cancer cell invasion, we here used 3D invasion culture of tumor spheroids in 3D fibrillar collagen and applied Ethanol-Ethyl cinnamate (EtOH-ECi) based optical clearing to detect both spheroid core and invasion zone by subcellular-resolved 3D microscopy. When subjected to a single dose of irradiation (4 Gy), we detected significant cell survival in the invasion zone. By physical separation of the core and invasion zone, we identified differentially regulated genes preferentially engaged in invading cells controlling cell division, repair, and survival. This imaging-based 3D invasion culture may be useful for the analysis of complex therapy-response patterns in cancer cells in drug discovery and invasion-associated resistance development. Supplementary Information The online version contains supplementary material available at 10.1007/s44164-022-00040-x.
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Affiliation(s)
- Felix Weiss
- Department of Cell Biology, Radboud University Medical Centre, P.O. Box 9101, 6525 GA Nijmegen, The Netherlands
| | - Nader Atlasy
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Vince van Reijmersdal
- Department of Cell Biology, Radboud University Medical Centre, P.O. Box 9101, 6525 GA Nijmegen, The Netherlands
| | - Henk Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Cornelia Hulsbergen-Veelken
- Department of Cell Biology, Radboud University Medical Centre, P.O. Box 9101, 6525 GA Nijmegen, The Netherlands
| | - Peter Friedl
- Department of Cell Biology, Radboud University Medical Centre, P.O. Box 9101, 6525 GA Nijmegen, The Netherlands
- David H. Koch Center for Applied Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
- Cancer Genomics Centre, 3584 CG Utrecht, The Netherlands
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13
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Zhan YJ, Zhang SW, Zhu S, Jiang N. Tissue Clearing and Its Application in the Musculoskeletal System. ACS OMEGA 2023; 8:1739-1758. [PMID: 36687066 PMCID: PMC9850472 DOI: 10.1021/acsomega.2c05180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The musculoskeletal system is an integral part of the human body. Currently, most skeletal muscle research is conducted through conventional histological sections due to technological limitations and the structure of skeletal muscles. For studying and observing bones and muscles, there is an urgent need for three-dimensional, objective imaging technologies. Optical tissue-clearing technologies seem to offer a novel and accessible approach to research of the musculoskeletal system. Using this approach, the components which cause refraction or prevent light from penetrating into the tissue are physically and chemically eliminated; then the liquid in the tissue is replaced with high-refractive-index chemicals. This innovative method, which allows three-dimensional reconstruction at the cellular and subcellular scale, significantly improves imaging depth and resolution. Nonetheless, this technology was not originally developed to image bones or muscles. When compared with brain and nerve organs which have attracted considerable attention in this field, the musculoskeletal system contains fewer lipids and has high levels of hemoglobin, collagen fibers, and inorganic hydroxyapatite crystals. Currently, three-dimensional imaging methods are widely used in the diagnosis and treatment of skeletal and muscular illnesses. In this regard, it is vitally important to review and evaluate the optical tissue-clearing technologies currently employed in the musculoskeletal system, so that researchers may make an informed decision. In the meantime, this study offers guidelines and recommendations for expanding the use of this technology in the musculoskeletal system.
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Affiliation(s)
- Yan-Jing Zhan
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Shi-Wen Zhang
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - SongSong Zhu
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Nan Jiang
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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14
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Kurz FT, Hahn A. Advanced Computational Methods to Evaluate Vascular Heterogeneity in Tumor Tissue Based on Single Plane Illumination Microscopy. Methods Mol Biol 2023; 2660:283-294. [PMID: 37191805 DOI: 10.1007/978-1-0716-3163-8_20] [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: 05/17/2023]
Abstract
During tumor growth, the complex composition of vasculature is prone to dynamic changes due to mechanic and biochemical challenges. Perivascular invasion of tumor cells to co-opt existing vasculature, but also formation of de-novo vasculature and other effects on the vascular network, may lead to altered geometric vessel properties as well as changes in vascular network topology, which is defined by vascular multifurcations and connections between vessel segments. The intricate organization and heterogeneity of the vascular network can be analyzed with advanced computational methods to uncover vascular network signatures that may allow differentiating between pathological and physiological vessel regions. Herein, we present a protocol to evaluate vascular heterogeneity in whole vascular networks, using morphological and topological measures. The protocol was developed for single plane illumination microscopy images of mice brain vasculature but can be applied to any vascular network.
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Affiliation(s)
- Felix T Kurz
- Division of Radiology, German Cancer Research Center, Heidelberg, Germany.
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15
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Lopes MM, Paysan J, Rino J, Lopes SM, Pereira de Almeida L, Cortes L, Nobre RJ. A new protocol for whole-brain biodistribution analysis of AAVs by tissue clearing, light-sheet microscopy and semi-automated spatial quantification. Gene Ther 2022; 29:665-679. [PMID: 36316447 DOI: 10.1038/s41434-022-00372-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 10/04/2022] [Accepted: 10/10/2022] [Indexed: 12/23/2022]
Abstract
Recombinant adeno-associated virus (rAAV) has become one of the most promising gene delivery systems for both in vitro and in vivo applications. However, a key challenge is the lack of suitable imaging technologies to evaluate delivery, biodistribution and tropism of rAAVs and efficiently monitor disease amelioration promoted by AAV-based therapies at a whole-organ level with single-cell resolution. Therefore, we aimed to establish a new pipeline for the biodistribution analysis of natural and new variants of AAVs at a whole-brain level by tissue clearing and light-sheet fluorescence microscopy (LSFM). To test this platform, neonatal C57BL/6 mice were intravenously injected with rAAV9 encoding EGFP and, after sacrifice, brains were processed by standard immunohistochemistry and a recently released aqueous-based clearing procedure. This clearing technique required no dedicated equipment and rendered highly cleared brains, while simultaneously preserving endogenous fluorescence. Moreover, three-dimensional imaging by LSFM allowed the quantitative analysis of EGFP at a whole-brain level, as well as the reconstruction of Purkinje cells for the retrieval of valuable morphological information inaccessible by standard immunohistochemistry. In conclusion, the pipeline herein described takes the AAVs to a new level when coupled to LSFM, proving its worth as a bioimaging tool in tropism and gene therapy studies.
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Affiliation(s)
- Miguel M Lopes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | | | - José Rino
- iMM - Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sara M Lopes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Luís Pereira de Almeida
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal. .,ViraVector - Viral Vectors for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal. .,FFUC - Faculty of Pharmacy of the University of Coimbra, Coimbra, Portugal.
| | - Luísa Cortes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal. .,IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal. .,MICC-CNC - Microscopy Imaging Center of Coimbra - CNC, University of Coimbra, Coimbra, Portugal.
| | - Rui Jorge Nobre
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal. .,IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal. .,ViraVector - Viral Vectors for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal.
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16
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Lu T, Shinozaki M, Nagoshi N, Nakamura M, Okano H. Long Preservation of AAV-Transduced Fluorescence by a Modified Organic Solvent-Based Clearing Method. Int J Mol Sci 2022; 23:ijms23179637. [PMID: 36077034 PMCID: PMC9455935 DOI: 10.3390/ijms23179637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/17/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022] Open
Abstract
The development of tissue clearing technologies allows 3D imaging of whole tissues and organs, especially in studies of the central nervous system innervated throughout the body. Although the three-dimensional imaging of solvent-cleared organs (3DISCO) method provides a powerful clearing capacity and high transparency, the rapid quenching of endogenous fluorescence and peroxide removal process decreases its practicability. This study provides a modified method named tDISCO to solve these limitations. The tDISCO protocol can preserve AAV-transduced endogenous EGFP fluorescence for months and achieve high transparency in a fast and simple clearing process. In addition to the brain, tDISCO was applied to other organs and even hard bone tissue. tDISCO also enabled us to visualize the long projection neurons and axons with high resolution. This method provides a fast and simple clearing protocol for 3D visualization of the AAV- transduced long projection neurons throughout the brain and spinal cord.
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Affiliation(s)
- Tao Lu
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Munehisa Shinozaki
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Narihito Nagoshi
- Department of Orthopaedic Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masaya Nakamura
- Department of Orthopaedic Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- Correspondence: (M.N.); (H.O.)
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- Correspondence: (M.N.); (H.O.)
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17
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Dyer L, Parker A, Paphiti K, Sanderson J. Lightsheet Microscopy. Curr Protoc 2022; 2:e448. [PMID: 35838628 DOI: 10.1002/cpz1.448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this paper, we review lightsheet (selective plane illumination) microscopy for mouse developmental biologists. There are different means of forming the illumination sheet, and we discuss these. We explain how we introduced the lightsheet microscope economically into our core facility and present our results on fixed and living samples. We also describe methods of clearing fixed samples for three-dimensional imaging and discuss the various means of preparing samples with particular reference to mouse cilia, adipose spheroids, and cochleae. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Laura Dyer
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Andrew Parker
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Keanu Paphiti
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
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18
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Hériché M, Arnould C, Wipf D, Courty PE. Imaging plant tissues: advances and promising clearing practices. TRENDS IN PLANT SCIENCE 2022; 27:601-615. [PMID: 35339361 DOI: 10.1016/j.tplants.2021.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The study of the organ structure of plants and understanding their physiological complexity requires 3D imaging with subcellular resolution. Most plant organs are highly opaque to light, and their study under optical sectioning microscopes is therefore difficult. In animals, many protocols have been developed to make organs transparent to light using clearing protocols (CPs). By contrast, clearing plant tissues is challenging because of the presence of fibers and pigments. We describe progress in the development of plant CPs over the past 20 years through a modified taxonomy of CPs based on their physical and optical parameters that affect tissue properties. We also discuss successful approaches that combine CPs with new microscopy methods and their future applications in plant science research.
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Affiliation(s)
- Mathilde Hériché
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Christine Arnould
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France.
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19
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Hahn A, Bode J, Schuhegger S, Krüwel T, Sturm VJF, Zhang K, Jende JME, Tews B, Heiland S, Bendszus M, Breckwoldt MO, Ziener CH, Kurz FT. Brain tumor classification of virtual NMR voxels based on realistic blood vessel-induced spin dephasing using support vector machines. NMR IN BIOMEDICINE 2022; 35:e4307. [PMID: 32289884 DOI: 10.1002/nbm.4307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 05/28/2023]
Abstract
Remodeling of tissue microvasculature commonly promotes neoplastic growth; however, there is no imaging modality in oncology yet that noninvasively quantifies microvascular changes in clinical routine. Although blood capillaries cannot be resolved in typical magnetic resonance imaging (MRI) measurements, their geometry and distribution influence the integral nuclear magnetic resonance (NMR) signal from each macroscopic MRI voxel. We have numerically simulated the expected transverse relaxation in NMR voxels with different dimensions based on the realistic microvasculature in healthy and tumor-bearing mouse brains (U87 and GL261 glioblastoma). The 3D capillary structure in entire, undissected brains was acquired using light sheet fluorescence microscopy to produce large datasets of the highly resolved cerebrovasculature. Using this data, we trained support vector machines to classify virtual NMR voxels with different dimensions based on the simulated spin dephasing accountable to field inhomogeneities caused by the underlying vasculature. In prediction tests with previously blinded virtual voxels from healthy brain tissue and GL261 tumors, stable classification accuracies above 95% were reached. Our results indicate that high classification accuracies can be stably attained with achievable training set sizes and that larger MRI voxels facilitated increasingly successful classifications, even with small training datasets. We were able to prove that, theoretically, the transverse relaxation process can be harnessed to learn endogenous contrasts for single voxel tissue type classifications on tailored MRI acquisitions. If translatable to experimental MRI, this may augment diagnostic imaging in oncology with automated voxel-by-voxel signal interpretation to detect vascular pathologies.
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Affiliation(s)
- Artur Hahn
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Physics and Astronomy, University of Heidelberg, Heidelberg, Germany
| | - Julia Bode
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
| | - Sarah Schuhegger
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Physics and Astronomy, University of Heidelberg, Heidelberg, Germany
| | - Thomas Krüwel
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
| | - Volker J F Sturm
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Radiology E010, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ke Zhang
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Radiology E010, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johann M E Jende
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Björn Tews
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
| | - Sabine Heiland
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael O Breckwoldt
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian H Ziener
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Radiology E010, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix T Kurz
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Radiology E010, German Cancer Research Center (DKFZ), Heidelberg, Germany
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20
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Eliat F, Sohn R, Renner H, Kagermeier T, Volkery S, Brinkmann H, Kirschnick N, Kiefer F, Grabos M, Becker K, Bedzhov I, Schöler HR, Bruder JM. Tissue clearing may alter emission and absorption properties of common fluorophores. Sci Rep 2022; 12:5551. [PMID: 35365729 PMCID: PMC8975997 DOI: 10.1038/s41598-022-09303-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 03/15/2022] [Indexed: 11/18/2022] Open
Abstract
In recent years, 3D cell culture has been gaining a more widespread following across many fields of biology. Tissue clearing enables optical analysis of intact 3D samples and investigation of molecular and structural mechanisms by homogenizing the refractive indices of tissues to make them nearly transparent. Here, we describe and quantify that common clearing solutions including benzyl alcohol/benzyl benzoate (BABB), PEG-associated solvent system (PEGASOS), immunolabeling-enabled imaging of solvent-cleared organs (iDISCO), clear, unobstructed brain/body imaging cocktails and computational analysis (CUBIC), and ScaleS4 alter the emission spectra of Alexa Fluor fluorophores and fluorescent dyes. Clearing modifies not only the emitted light intensity but also alters the absorption and emission peaks, at times to several tens of nanometers. The resulting shifts depend on the interplay of solvent, fluorophore, and the presence of cells. For biological applications, this increases the risk for unexpected channel crosstalk, as filter sets are usually not optimized for altered fluorophore emission spectra in clearing solutions. This becomes especially problematic in high throughput/high content campaigns, which often rely on multiband excitation to increase acquisition speed. Consequently, researchers relying on clearing in quantitative multiband excitation experiments should crosscheck their fluorescent signal after clearing in order to inform the proper selection of filter sets and fluorophores for analysis.
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Affiliation(s)
- Farsam Eliat
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany.,University of Münster, Schlossplatz 2, 48143, Münster, Germany
| | - Rebecca Sohn
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Henrik Renner
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Theresa Kagermeier
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany.,University of Münster, Schlossplatz 2, 48143, Münster, Germany
| | - Stefan Volkery
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Heike Brinkmann
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Nils Kirschnick
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany.,University of Münster, European Institute for Molecular Imaging, Waldeyerstraße 15, 48149, Münster, Germany
| | - Friedemann Kiefer
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany.,University of Münster, European Institute for Molecular Imaging, Waldeyerstraße 15, 48149, Münster, Germany
| | - Martha Grabos
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Katharina Becker
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany.,University of Münster, Schlossplatz 2, 48143, Münster, Germany
| | - Ivan Bedzhov
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany
| | - Jan M Bruder
- Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149, Münster, Germany.
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21
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Shan QH, Qin XY, Zhou N, Huang C, Wang Y, Chen P, Zhou JN. A method for ultrafast tissue clearing that preserves fluorescence for multimodal and longitudinal brain imaging. BMC Biol 2022; 20:77. [PMID: 35351101 PMCID: PMC8966190 DOI: 10.1186/s12915-022-01275-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 03/09/2022] [Indexed: 11/25/2022] Open
Abstract
Background Tissue-clearing techniques have recently been developed to make tissues transparent for three-dimensional (3D) imaging at different scales, including single-cell resolution. However, current tissue-clearing workflows have several disadvantages, including complex protocols, time-consuming application, and fluorescence quenching. Additionally, they can be used mainly for clearing larger-volume samples, preventing wide and easy applicability in conventional experimental approaches. In this study, we aimed to develop a versatile, fast, and convenient method for clearing thin and semi-thick samples, which can be used for three-dimensional imaging of experimental or even clinical samples. Results We developed an alkaline solution (AKS) containing a combination of 2,2′-thiodiethanol (TDE), DMSO, D-sorbitol, and Tris for tissue clearing, as the alkaline environment is suitable for maintaining the fluorescence of most commonly used fluorescence protein GFP and its variants, and tested its clearing effect on samples from mice and human brains. We assessed the clearing speed, the preservation of fluorescence protein and dyes, and the imaging depth and quality. The results showed that AKS treatment rapidly cleared 300-μm-thick brain slices and 1-mm-thick slices from different organs within 5 min and 1 h, respectively. Moreover, AKS was compatible with a variety of fluorescence proteins and dyes. Most importantly, AKS enhanced the fluorescence of YFP, in contrast to the majority of existing tissue-clearing methods which reduce the fluorescence intensity of fluorescent proteins. Using AKS, we performed long-time high-resolution imaging of weak fluorescent protein-labelled tissues, long-distance fibre tracking, larger-scale 3D imaging and cell counting of the entire brain area, neural circuit tracing, 3D neuromorphic reconstruction, and 3D histopathology imaging. Conclusions AKS can be used for simple and rapid clearing of samples from mice and human brains and is widely compatible with a variety of fluorescent dyes. Therefore, AKS has great potential to be used as a broad tissue-clearing reagent for biological optical imaging, especially for time-sensitive experiments. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01275-6.
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Affiliation(s)
- Qing-Hong Shan
- Chinese Academy of Science Key Laboratory of Brain Function and Diseases, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Xin-Ya Qin
- Chinese Academy of Science Key Laboratory of Brain Function and Diseases, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Nan Zhou
- Department of Neurosurgery, Huashan Hospital, Fudan University, Middle Urumqi Road 12, Shanghai, 200040, China
| | - Chuan Huang
- Chinese Academy of Science Key Laboratory of Brain Function and Diseases, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Yu Wang
- Chinese Academy of Science Key Laboratory of Brain Function and Diseases, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Peng Chen
- Chinese Academy of Science Key Laboratory of Brain Function and Diseases, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Jiang-Ning Zhou
- Chinese Academy of Science Key Laboratory of Brain Function and Diseases, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China. .,Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
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22
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Richardson DS, Guan W, Matsumoto K, Pan C, Chung K, Ertürk A, Ueda HR, Lichtman JW. TISSUE CLEARING. NATURE REVIEWS. METHODS PRIMERS 2022; 1. [PMID: 35128463 DOI: 10.1038/s43586-021-00080-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Tissue clearing of gross anatomical samples was first described over a century ago and has only recently found widespread use in the field of microscopy. This renaissance has been driven by the application of modern knowledge of optical physics and chemical engineering to the development of robust and reproducible clearing techniques, the arrival of new microscopes that can image large samples at cellular resolution and computing infrastructure able to store and analyze large data volumes. Many biological relationships between structure and function require investigation in three dimensions and tissue clearing therefore has the potential to enable broad discoveries in the biological sciences. Unfortunately, the current literature is complex and could confuse researchers looking to begin a clearing project. The goal of this Primer is to outline a modular approach to tissue clearing that allows a novice researcher to develop a customized clearing pipeline tailored to their tissue of interest. Further, the Primer outlines the required imaging and computational infrastructure needed to perform tissue clearing at scale, gives an overview of current applications, discusses limitations and provides an outlook on future advances in the field.
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Affiliation(s)
- Douglas S Richardson
- Harvard Center for Biological Imaging, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Webster Guan
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
| | - Katsuhiko Matsumoto
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Chenchen Pan
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians University of Munich, Munich, Germany.,Graduate School of Systemic Neurosciences (GSN), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Kwanghun Chung
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.,Broad Institute of Harvard University and MIT, Cambridge, MA, USA.,Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.,Nano Biomedical Engineering (Nano BME) Graduate Program, Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Ali Ertürk
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians University of Munich, Munich, Germany.,Graduate School of Systemic Neurosciences (GSN), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Jeff W Lichtman
- Harvard Center for Biological Imaging, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Center for Brain Science, Harvard University, Cambridge, MA, USA
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23
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Woo J, Lee EY, Lee M, Ku S, Park JY, Cho YE. Comparative Analyses of Clearing Efficacies of Tissue Clearing Protocols by Using a Punching Assisted Clarity Analysis. Front Bioeng Biotechnol 2022; 9:784626. [PMID: 35155401 PMCID: PMC8831720 DOI: 10.3389/fbioe.2021.784626] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/30/2021] [Indexed: 02/03/2023] Open
Abstract
The advent of tissue clearing methods, in conjunction with novel high-resolution imaging techniques, has enabled the visualization of three-dimensional structures with unprecedented depth and detail. Although a variety of clearing protocols have been developed, little has been done to quantify their efficacies in a systematic, reproducible fashion. Here, we present two simple assays, Punching-Assisted Clarity Analysis (PACA)-Light and PACA-Glow, which use easily accessible spectroscopy and gel documentation systems to quantify the transparency of multiple cleared tissues simultaneously. We demonstrate the use of PACA-Light and PACA-Glow to compare twenty-eight tissue clearing protocols on rodent brains. We also show that regional differences exist in tissue transparency in the rodent brain, with cerebellar tissue consistently achieving lower clearing levels compared to the prefrontal or cerebral cortex across all protocols. This represents the largest comparative study of tissue clearing protocols to date, made possible by the high-throughput nature of our PACA platforms.
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Affiliation(s)
- Jiwon Woo
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Institute, Biohedron Therapeutics Co., Ltd., Seoul, South Korea
| | - Eunice Yoojin Lee
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Mirae Lee
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Seockmo Ku
- Fermentation Science Program, School of Agriculture, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Jeong-Yoon Park
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Yong Eun Cho
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- *Correspondence: Yong Eun Cho,
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24
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Monticelli SR, Bryk P, Brewer MG, Aguilar HC, Norbury CC, Ward BM. An increase in glycoprotein concentration on extracellular virions dramatically alters vaccinia virus infectivity and pathogenesis without impacting immunogenicity. PLoS Pathog 2021; 17:e1010177. [PMID: 34962975 PMCID: PMC8746760 DOI: 10.1371/journal.ppat.1010177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/10/2022] [Accepted: 12/02/2021] [Indexed: 11/20/2022] Open
Abstract
The extracellular virion (EV) form of Orthopoxviruses is required for cell-to-cell spread and pathogenesis, and is the target of neutralizing antibodies in the protective immune response. EV have a double envelope that contains several unique proteins that are involved in its intracellular envelopment and/or subsequent infectivity. One of these, F13, is involved in both EV formation and infectivity. Here, we report that replacement of vaccinia virus F13L with the molluscum contagiosum virus homolog, MC021L, results in the production of EV particles with significantly increased levels of EV glycoproteins, which correlate with a small plaque phenotype. Using a novel fluorescence-activated virion sorting assay to isolate EV populations based on glycoprotein content we determine that EV containing either higher or lower levels of glycoproteins are less infectious, suggesting that there is an optimal concentration of glycoproteins in the outer envelope that is required for maximal infectivity of EV. This optimal glycoprotein concentration was required for lethality and induction of pathology in a cutaneous model of animal infection, but was not required for induction of a protective immune response. Therefore, our results demonstrate that there is a sensitive balance between glycoprotein incorporation, infectivity, and pathogenesis, and that manipulation of EV glycoprotein levels can produce vaccine vectors in which pathologic side effects are attenuated without a marked diminution in induction of protective immunity. Viral glycoproteins are critical determinants of host cell tropism, immunity, and pathogenesis. Vaccinia virus was used for the most successful immunization program in history, and poxviruses continue to be used as vaccine vectors. Here, we report that vaccinia virus extracellular virion (EV) protein F13 plays an important, previously unappreciated, role in controlling glycoprotein incorporation, and that there is a direct relationship between glycoprotein concentrations and subsequent infectivity. Crucially, manipulation of the EV glycoprotein concentrations altered pathogenesis and lethality in an in vivo infection model, but did not markedly alter the induced immune response. These results have important implications that inform the design of safer and more efficacious poxvirus-based vaccine vectors by altering glycoprotein content.
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Affiliation(s)
- Stephanie R. Monticelli
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Peter Bryk
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Matthew G. Brewer
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Hector C. Aguilar
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York, United States of America
| | - Christopher C. Norbury
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Brian M. Ward
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail:
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25
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Di Castro MA, Volterra A. Astrocyte control of the entorhinal cortex-dentate gyrus circuit: Relevance to cognitive processing and impairment in pathology. Glia 2021; 70:1536-1553. [PMID: 34904753 PMCID: PMC9299993 DOI: 10.1002/glia.24128] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022]
Abstract
The entorhinal cortex-dentate gyrus circuit is centrally involved in memory processing conveying to the hippocampus spatial and nonspatial context information via, respectively, medial and lateral perforant path (MPP and LPP) excitatory projections onto dentate granule cells (GCs). Here, we review work of several years from our group showing that astrocytes sense local synaptic transmission and exert in turn a presynaptic control at PP-GC synapses. Modulation of neurotransmitter release probability by astrocytes sets basal synaptic strength and dynamic range for long-term potentiation of PP-GC synapses. Intriguingly, this astrocyte control is circuit-specific, being present only at MPP-GC (not LPP-GC) synapses, which selectively express atypical presynaptic N-methyl-D-aspartate receptors (NMDAR) suitable to activation by astrocyte-released glutamate. Moreover, the astrocytic control is peculiarly dependent on the cytokine TNFα, which at constitutive levels acts as a gating factor for the astrocyte signaling. During inflammation/infection processes, increased levels of TNFα lead to uncontrolled astrocyte glutamate release, altered PP-GC circuit processing and, ultimately, impaired contextual memory performance. The TNFα-dependent pathological switch of the synaptic control from astrocytes and its deleterious consequences are observed in animal models of HIV brain infection and multiple sclerosis, conditions both known to cause cognitive disturbances in up to 50% of patients. The review also discusses open issues related to the identified astrocytic pathway: its role in contextual memory processing, potential damaging role in Alzheimer's disease, the existence of vesicular glutamate release from DG astrocytes, and the possible synaptic-like connectivity between astrocytic output sites and PP receptive sites.
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Affiliation(s)
- Maria Amalia Di Castro
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland.,Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Andrea Volterra
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
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26
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Kosmidis S, Negrean A, Dranovsky A, Losonczy A, Kandel ER. A fast, aqueous, reversible three-day tissue clearing method for adult and embryonic mouse brain and whole body. CELL REPORTS METHODS 2021; 1:100090. [PMID: 34966901 PMCID: PMC8713566 DOI: 10.1016/j.crmeth.2021.100090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/13/2021] [Accepted: 09/03/2021] [Indexed: 12/23/2022]
Abstract
Optical clearing methods serve as powerful tools to study intact organs and neuronal circuits. We developed an aqueous clearing protocol, Fast 3D Clear, that relies on tetrahydrofuran for tissue delipidation and iohexol for clearing, such that tissues can be imaged under immersion oil in light-sheet imaging systems. Fast 3D Clear requires 3 days to achieve high transparency of adult and embryonic mouse tissues while maintaining their anatomical integrity and preserving a vast array of transgenic and viral/dye fluorophores. A unique advantage of Fast 3D Clear is its complete reversibility and thus compatibility with tissue sectioning and immunohistochemistry. Fast 3D Clear can be easily and quickly applied to a wide range of biomedical studies, facilitating the acquisition of high-resolution two- and three-dimensional images.
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Affiliation(s)
- Stylianos Kosmidis
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
- Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Adrian Negrean
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Alex Dranovsky
- New York State Psychiatric Institute, New York, NY 10032, USA; Department of Psychiatry, Columbia University, New York, NY 10032, USA
| | - Attila Losonczy
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Eric R. Kandel
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
- Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
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27
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Endo M, Maruoka H, Okabe S. Advanced Technologies for Local Neural Circuits in the Cerebral Cortex. Front Neuroanat 2021; 15:757499. [PMID: 34803616 PMCID: PMC8595196 DOI: 10.3389/fnana.2021.757499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
The neural network in the brain can be viewed as an integrated system assembled from a large number of local neural circuits specialized for particular brain functions. Activities of neurons in local neural circuits are thought to be organized both spatially and temporally under the rules optimized for their roles in information processing. It is well perceived that different areas of the mammalian neocortex have specific cognitive functions and distinct computational properties. However, the organizational principles of the local neural circuits in different cortical regions have not yet been clarified. Therefore, new research principles and related neuro-technologies that enable efficient and precise recording of large-scale neuronal activities and synaptic connections are necessary. Innovative technologies for structural analysis, including tissue clearing and expansion microscopy, have enabled super resolution imaging of the neural circuits containing thousands of neurons at a single synapse resolution. The imaging resolution and volume achieved by new technologies are beyond the limits of conventional light or electron microscopic methods. Progress in genome editing and related technologies has made it possible to label and manipulate specific cell types and discriminate activities of multiple cell types. These technologies will provide a breakthrough for multiscale analysis of the structure and function of local neural circuits. This review summarizes the basic concepts and practical applications of the emerging technologies and new insight into local neural circuits obtained by these technologies.
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Affiliation(s)
| | | | - Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
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28
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Almagro J, Messal HA, Zaw Thin M, van Rheenen J, Behrens A. Tissue clearing to examine tumour complexity in three dimensions. Nat Rev Cancer 2021; 21:718-730. [PMID: 34331034 DOI: 10.1038/s41568-021-00382-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/18/2021] [Indexed: 02/07/2023]
Abstract
The visualization of whole organs and organisms through tissue clearing and fluorescence volumetric imaging has revolutionized the way we look at biological samples. Its application to solid tumours is changing our perception of tumour architecture, revealing signalling networks and cell interactions critical in tumour progression, and provides a powerful new strategy for cancer diagnostics. This Review introduces the latest advances in tissue clearing and three-dimensional imaging, examines the challenges in clearing epithelia - the tissue of origin of most malignancies - and discusses the insights that tissue clearing has brought to cancer research, as well as the prospective applications to experimental and clinical oncology.
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Affiliation(s)
- Jorge Almagro
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | - Hendrik A Messal
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - May Zaw Thin
- Cancer Stem Cell Laboratory, Institute of Cancer Research, London, UK
| | - Jacco van Rheenen
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Axel Behrens
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK.
- Cancer Stem Cell Laboratory, Institute of Cancer Research, London, UK.
- Convergence Science Centre and Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK.
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29
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Schwarz MK, Kubitscheck U. Expansion light sheet fluorescence microscopy of extended biological samples: Applications and perspectives. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 168:33-36. [PMID: 34626664 DOI: 10.1016/j.pbiomolbio.2021.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/25/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Martin K Schwarz
- Institute Experimental Epileptology and Cognition Research (EECR), University of Bonn Medical School, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
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30
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Zhu J, Liu X, Deng Y, Li D, Yu T, Zhu D. Tissue optical clearing for 3D visualization of vascular networks: A review. Vascul Pharmacol 2021; 141:106905. [PMID: 34506969 DOI: 10.1016/j.vph.2021.106905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/01/2022]
Abstract
Reconstruction of the vasculature of intact tissues/organs down to the capillary level is essential for understanding the development and remodeling of vascular networks under physiological and pathological conditions. Optical imaging techniques can provide sufficient resolution to distinguish small vessels with several microns, but the imaging depth is somewhat limited due to the high light scattering of opaque tissue. Recently, various tissue optical clearing methods have been developed to overcome light attenuation and improve the imaging depth both for ex-vivo and in-vivo visualizations. Tissue clearing combined with vessel labeling techniques and advanced optical tomography enables successful mapping of the vasculature of different tissues/organs, as well as dynamically monitoring vessel function under normal and pathological conditions. Here, we briefly introduce the commonly-used labeling strategies for entire vascular networks, the current tissue optical clearing techniques available for various tissues, as well as the advanced optical imaging techniques for fast, high-resolution structural and functional imaging for blood vessels. We also discuss the applications of these techniques in the 3D visualization of vascular networks in normal tissues, and the vascular remodeling in several typical pathological models in clinical research. This review is expected to provide valuable insights for researchers to study the potential mechanisms of various vessel-associated diseases using tissue optical clearing pipeline.
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Affiliation(s)
- Jingtan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaomei Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yating Deng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dongyu Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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31
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Abstract
Tissue clearing increases the transparency of late developmental stages and enables deep imaging in fixed organisms. Successful implementation of these methodologies requires a good grasp of sample processing, imaging and the possibilities offered by image analysis. In this Primer, we highlight how tissue clearing can revolutionize the histological analysis of developmental processes and we advise on how to implement effective clearing protocols, imaging strategies and analysis methods for developmental biology.
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Affiliation(s)
| | - Nicolas Renier
- Sorbonne Université, Paris Brain Institute – ICM, INSERM, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
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32
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Basic principles of hydrogel-based tissue transformation technologies and their applications. Cell 2021; 184:4115-4136. [PMID: 34358468 DOI: 10.1016/j.cell.2021.07.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/06/2021] [Accepted: 07/06/2021] [Indexed: 12/28/2022]
Abstract
Emerging tissue transformation technologies provide an unprecedented opportunity to investigate system-level molecular and anatomical features in situ. Hydrogel-based methods engineer physicochemical tissue properties to render intact organs optically transparent and size and shape adjustable while preserving biomolecules at their physiological locations. When combined with advanced molecular tools, labeling, and imaging techniques, tissue transformation enables three-dimensional (3D) mapping of molecules, cells, and their interrelationships at increasing speeds and resolutions. In this review, we discuss the basic engineering principles of tissue transformation and labeling techniques as well as their broad applications, current challenges, and future potential.
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33
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Hahn A, Bode J, Alexander A, Karimian-Jazi K, Schregel K, Schwarz D, Sommerkamp AC, Krüwel T, Abdollahi A, Wick W, Platten M, Bendszus M, Tews B, Kurz FT, Breckwoldt MO. Large-scale characterization of the microvascular geometry in development and disease by tissue clearing and quantitative ultramicroscopy. J Cereb Blood Flow Metab 2021; 41:1536-1546. [PMID: 33043767 PMCID: PMC8217891 DOI: 10.1177/0271678x20961854] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 08/04/2020] [Accepted: 08/30/2020] [Indexed: 12/16/2022]
Abstract
Three-dimensional assessment of optically cleared, entire organs and organisms has recently become possible by tissue clearing and selective plane illumination microscopy ("ultramicroscopy"). Resulting datasets can be highly complex, encompass over a thousand images with millions of objects and data of several gigabytes per acquisition. This constitutes a major challenge for quantitative analysis. We have developed post-processing tools to quantify millions of microvessels and their distribution in three-dimensional datasets from ultramicroscopy and demonstrate the capabilities of our pipeline within entire mouse brains and embryos. Using our developed acquisition, segmentation, and analysis platform, we quantify physiological vascular networks in development and the healthy brain. We compare various geometric vessel parameters (e.g. vessel density, radius, tortuosity) in the embryonic spinal cord and brain as well as in different brain regions (basal ganglia, corpus callosum, cortex). White matter tract structures (corpus callosum, spinal cord) showed lower microvascular branch densities and longer vessel branch length compared to grey matter (cortex, basal ganglia). Furthermore, we assess tumor neoangiogenesis in a mouse glioma model to compare tumor core and tumor border. The developed methodology allows rapid quantification of three-dimensional datasets by semi-automated segmentation of fluorescently labeled objects with conventional computer hardware. Our approach can aid preclinical investigations and paves the way towards "quantitative ultramicroscopy".
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Affiliation(s)
- Artur Hahn
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
- Department of Physics and Astronomy, University of Heidelberg, Heidelberg, Germany
| | - Julia Bode
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
| | - Allen Alexander
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Katharina Schregel
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel Schwarz
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Alexander C Sommerkamp
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Thomas Krüwel
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
| | - Amir Abdollahi
- German Cancer Consortium and Heidelberg Institute of Radiation Oncology, National Center for Radiation Research in Oncology, Heidelberg, Germany
- Heidelberg University School of Medicine, Heidelberg University, Heidelberg, Germany
- Translational Radiation Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Wick
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology, University Medical Center Mannheim, Heidelberg University, Heidelberg, Germany
| | - Martin Bendszus
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Björn Tews
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
| | - Felix T Kurz
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael O Breckwoldt
- Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Wan P, Li Y, Zhu J, Xu J, Liu X, Yu T, Zhu D. FDISCO+: a clearing method for robust fluorescence preservation of cleared samples. NEUROPHOTONICS 2021; 8:035007. [PMID: 34514032 PMCID: PMC8427119 DOI: 10.1117/1.nph.8.3.035007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/24/2021] [Indexed: 05/05/2023]
Abstract
Significance: The recently reported solvent-based optical clearing method FDISCO can preserve various fluorescent signals very well. However, the strict low-temperature storage condition of FDISCO is not conducive to long-time or repetitive imaging usually conducted at room temperature. Therefore, it is important to solve the contradiction between fluorescence preservation and imaging condition. Aim: We develop a modified FDISCO clearing method, termed FDISCO+, to change the preservation condition from low temperature to room temperature. Approach: Two alternative antioxidants were screened out to effectively inhibit the peroxide generation in the clearing agent at room temperature, enabling robust fluorescence preservation of cleared samples. Results: FDISCO+ achieves comparable fluorescence preservation with the original FDISCO protocol and allows long-time storage at room temperature, making it easier for researchers to image and preserve the samples. Conclusions: FDISCO+ is expected to be widely used due to its loose operation requirements.
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Affiliation(s)
- Peng Wan
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
| | - Yusha Li
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
| | - Jingtan Zhu
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
| | - Jianyi Xu
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
| | - Xiaomei Liu
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
| | - Tingting Yu
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
- Address all correspondence to Tingting Yu,
| | - Dan Zhu
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
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Kirschnick N, Drees D, Redder E, Erapaneedi R, Pereira da Graca A, Schäfers M, Jiang X, Kiefer F. Rapid methods for the evaluation of fluorescent reporters in tissue clearing and the segmentation of large vascular structures. iScience 2021; 24:102650. [PMID: 34151237 PMCID: PMC8192726 DOI: 10.1016/j.isci.2021.102650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/23/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
Light sheet fluorescence microscopy (LSFM) of large tissue samples does not require mechanical sectioning and allows efficient visualization of spatially complex or rare structures. Therefore, LSFM has become invaluable in developmental and biomedical research. Because sample size may limit whole-mount staining, LSFM benefits from transgenic reporter organisms expressing fluorescent proteins (FPs) and, however, requires optical clearing and computational data visualization and analysis. The former often interferes with FPs, while the latter requires massive computing resources. Here, we describe 3D-polymerized cell dispersions, a rapid and straightforward method, based on recombinant FP expression in freely selectable tester cells, to evaluate and compare fluorescence retention in different tissue-clearing protocols. For the analysis of large LSFM data, which usually requires huge computing resources, we introduce a refined, interactive, hierarchical random walker approach that is capable of efficient segmentation of the vasculature in data sets even on a consumer grade PC.
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Affiliation(s)
- Nils Kirschnick
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Dominik Drees
- Institute of Computer Science, University of Münster, Einsteinstraße 62, 48149 Münster, Germany
| | - Esther Redder
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Raghu Erapaneedi
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Abel Pereira da Graca
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Michael Schäfers
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Xiaoyi Jiang
- Institute of Computer Science, University of Münster, Einsteinstraße 62, 48149 Münster, Germany
| | - Friedemann Kiefer
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
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Matryba P, Łukasiewicz K, Pawłowska M, Tomczuk J, Gołąb J. Can Developments in Tissue Optical Clearing Aid Super-Resolution Microscopy Imaging? Int J Mol Sci 2021; 22:ijms22136730. [PMID: 34201632 PMCID: PMC8268743 DOI: 10.3390/ijms22136730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
The rapid development of super-resolution microscopy (SRM) techniques opens new avenues to examine cell and tissue details at a nanometer scale. Due to compatibility with specific labelling approaches, in vivo imaging and the relative ease of sample preparation, SRM appears to be a valuable alternative to laborious electron microscopy techniques. SRM, however, is not free from drawbacks, with the rapid quenching of the fluorescence signal, sensitivity to spherical aberrations and light scattering that typically limits imaging depth up to few micrometers being the most pronounced ones. Recently presented and robustly optimized sets of tissue optical clearing (TOC) techniques turn biological specimens transparent, which greatly increases the tissue thickness that is available for imaging without loss of resolution. Hence, SRM and TOC are naturally synergistic techniques, and a proper combination of these might promptly reveal the three-dimensional structure of entire organs with nanometer resolution. As such, an effort to introduce large-scale volumetric SRM has already started; in this review, we discuss TOC approaches that might be favorable during the preparation of SRM samples. Thus, special emphasis is put on TOC methods that enhance the preservation of fluorescence intensity, offer the homogenous distribution of molecular probes, and vastly decrease spherical aberrations. Finally, we review examples of studies in which both SRM and TOC were successfully applied to study biological systems.
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Affiliation(s)
- Paweł Matryba
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
- The Doctoral School of the Medical University of Warsaw, Medical University of Warsaw, 02-097 Warsaw, Poland
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Correspondence:
| | - Kacper Łukasiewicz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
| | - Monika Pawłowska
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Jacek Tomczuk
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
| | - Jakub Gołąb
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
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37
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Susaki EA, Takasato M. Perspective: Extending the Utility of Three-Dimensional Organoids by Tissue Clearing Technologies. Front Cell Dev Biol 2021; 9:679226. [PMID: 34195197 PMCID: PMC8236633 DOI: 10.3389/fcell.2021.679226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 01/06/2023] Open
Abstract
An organoid, a self-organizing organ-like tissue developed from stem cells, can exhibit a miniaturized three-dimensional (3D) structure and part of the physiological functions of the original organ. Due to the reproducibility of tissue complexity and ease of handling, organoids have replaced real organs and animals for a variety of uses, such as investigations of the mechanisms of organogenesis and disease onset, and screening of drug effects and/or toxicity. The recent advent of tissue clearing and 3D imaging techniques have great potential contributions to organoid studies by allowing the collection and analysis of 3D images of whole organoids with a reasonable throughput and thus can expand the means of examining the 3D architecture, cellular components, and variability among organoids. Genetic and histological cell-labeling methods, together with organoid clearing, also allow visualization of critical structures and cellular components within organoids. The collected 3D data may enable image analysis to quantitatively assess structures within organoids and sensitively/effectively detect abnormalities caused by perturbations. These capabilities of tissue/organoid clearing and 3D imaging techniques not only extend the utility of organoids in basic biology but can also be applied for quality control of clinical organoid production and large-scale drug screening.
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Affiliation(s)
- Etsuo A. Susaki
- Department of Biochemistry and Systems Biomedicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Minoru Takasato
- Laboratory for Human Organogenesis, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Laboratory of Molecular Cell Biology and Development, Department of Animal Development and Physiology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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38
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Colombini M, Pasierbek P, Masselink W. A safe and reusable imaging chamber compatible with organic solvents. ACTA ACUST UNITED AC 2021; 69:321-323. [PMID: 32332999 DOI: 10.1093/jmicro/dfaa020] [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: 03/05/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 11/12/2022]
Abstract
High refractive index organic solvents are commonly used as an imaging medium in tissue clearing approaches. While effective, such solvents provide serious concerns for the safety of users and the equipment, especially in a central microscopy unit. To overcome these concerns, we have developed a large and reusable imaging chamber compatible with the universal mounting frame AK (PeCon GmbH). This chamber is easy to assemble and significantly improves the working environment in a central microscopy unit, where hazardous chemicals could negatively affect equipment and people. To encourage the uptake of these chambers, the design is made publicly available for download.
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Affiliation(s)
- Martin Colombini
- Research Institute of Molecular Pathology, Vienna BioCenter, Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Pawel Pasierbek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Wouter Masselink
- Research Institute of Molecular Pathology, Vienna BioCenter, Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
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Yu T, Li D, Zhu D. Tissue Optical Clearing for Biomedical Imaging: From In Vitro to In Vivo. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 3233:217-255. [PMID: 34053030 DOI: 10.1007/978-981-15-7627-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tissue optical clearing technique provides a prospective solution for the application of advanced optical methods in life sciences. This chapter firstly gives a brief introduction to mechanisms of tissue optical clearing techniques, from the physical mechanism to chemical mechanism, which is the most important foundation to develop tissue optical clearing methods. During the past years, in vitro and in vivo tissue optical clearing methods were developed. In vitro tissue optical clearing techniques, including the solvent-based clearing methods and the hydrophilic reagents-based clearing methods, combined with labeling technique and advanced microscopy, can be applied to image 3D microstructure of tissue blocks or whole organs such as brain and spinal cord with high resolution. In vivo skin or skull optical clearing, promise various optical imaging techniques to detect cutaneous or cortical cell and vascular structure and function without surgical window.
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Affiliation(s)
- Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dongyu Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China. .,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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40
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A deep learning algorithm for 3D cell detection in whole mouse brain image datasets. PLoS Comput Biol 2021; 17:e1009074. [PMID: 34048426 PMCID: PMC8191998 DOI: 10.1371/journal.pcbi.1009074] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 06/10/2021] [Accepted: 05/12/2021] [Indexed: 12/29/2022] Open
Abstract
Understanding the function of the nervous system necessitates mapping the spatial distributions of its constituent cells defined by function, anatomy or gene expression. Recently, developments in tissue preparation and microscopy allow cellular populations to be imaged throughout the entire rodent brain. However, mapping these neurons manually is prone to bias and is often impractically time consuming. Here we present an open-source algorithm for fully automated 3D detection of neuronal somata in mouse whole-brain microscopy images using standard desktop computer hardware. We demonstrate the applicability and power of our approach by mapping the brain-wide locations of large populations of cells labeled with cytoplasmic fluorescent proteins expressed via retrograde trans-synaptic viral infection.
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41
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Kolesová H, Olejníčková V, Kvasilová A, Gregorovičová M, Sedmera D. Tissue clearing and imaging methods for cardiovascular development. iScience 2021; 24:102387. [PMID: 33981974 PMCID: PMC8086021 DOI: 10.1016/j.isci.2021.102387] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tissue imaging in 3D using visible light is limited and various clearing techniques were developed to increase imaging depth, but none provides universal solution for all tissues at all developmental stages. In this review, we focus on different tissue clearing methods for 3D imaging of heart and vasculature, based on chemical composition (solvent-based, simple immersion, hyperhydration, and hydrogel embedding techniques). We discuss in detail compatibility of various tissue clearing techniques with visualization methods: fluorescence preservation, immunohistochemistry, nuclear staining, and fluorescent dyes vascular perfusion. We also discuss myocardium visualization using autofluorescence, tissue shrinking, and expansion. Then we overview imaging methods used to study cardiovascular system and live imaging. We discuss heart and vessels segmentation methods and image analysis. The review covers the whole process of cardiovascular system 3D imaging, starting from tissue clearing and its compatibility with various visualization methods to the types of imaging methods and resulting image analysis.
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Affiliation(s)
- Hana Kolesová
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
| | - Veronika Olejníčková
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
| | - Alena Kvasilová
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martina Gregorovičová
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
| | - David Sedmera
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
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Taranda J, Turcan S. 3D Whole-Brain Imaging Approaches to Study Brain Tumors. Cancers (Basel) 2021; 13:cancers13081897. [PMID: 33920839 PMCID: PMC8071100 DOI: 10.3390/cancers13081897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Brain tumors integrate into the brain and consist of tumor cells with different molecular alterations. During brain tumor pathogenesis, a variety of cell types surround the tumors to either inhibit or promote tumor growth. These cells are collectively referred to as the tumor microenvironment. Three-dimensional and/or longitudinal visualization approaches are needed to understand the growth of these tumors in time and space. In this review, we present three imaging modalities that are suitable or that can be adapted to study the volumetric distribution of malignant or tumor-associated cells in the brain. In addition, we highlight the potential clinical utility of some of the microscopy approaches for brain tumors using exemplars from solid tumors. Abstract Although our understanding of the two-dimensional state of brain tumors has greatly expanded, relatively little is known about their spatial structures. The interactions between tumor cells and the tumor microenvironment (TME) occur in a three-dimensional (3D) space. This volumetric distribution is important for elucidating tumor biology and predicting and monitoring response to therapy. While static 2D imaging modalities have been critical to our understanding of these tumors, studies using 3D imaging modalities are needed to understand how malignant cells co-opt the host brain. Here we summarize the preclinical utility of in vivo imaging using two-photon microscopy in brain tumors and present ex vivo approaches (light-sheet fluorescence microscopy and serial two-photon tomography) and highlight their current and potential utility in neuro-oncology using data from solid tumors or pathological brain as examples.
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Zhan Y, Wu H, Liu L, Lin J, Zhang S. Organic solvent-based tissue clearing techniques and their applications. JOURNAL OF BIOPHOTONICS 2021; 14:e202000413. [PMID: 33715302 DOI: 10.1002/jbio.202000413] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 02/05/2023]
Abstract
Revealing the true structure of tissues and organs with tissue slicing technology is difficult since images reconstructed in three dimensions are easily distorted. To address the limitations in tissue slicing technology, tissue clearing has been invented and has recently achieved significant progress in three-dimensional imaging. Currently, this technology can mainly be divided into two types: aqueous clearing methods and solvent-based clearing methods. As one of the important parts of this technology, organic solvent-based tissue clearing techniques have been widely applied because of their efficient clearing speed and high clearing intensity. This review introduces the primary organic solvent-based tissue clearing techniques and their applications.
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Affiliation(s)
- Yanjing Zhan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Haoyan Wu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Linfeng Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jie Lin
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shiwen Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Abstract
Advanced optical methods combined with various probes pave the way toward molecular imaging within living cells. However, major challenges are associated with the need to enhance the imaging resolution even further to the subcellular level for the imaging of larger tissues, as well as for in vivo studies. High scattering and absorption of opaque tissues limit the penetration of light into deep tissues and thus the optical imaging depth. Tissue optical clearing technique provides an innovative way to perform deep-tissue imaging. Recently, various optical clearing methods have been developed, which provide tissue clearing based on similar physical principles via different chemical approaches. Here, we introduce the mechanisms of the current clearing methods from fundamental physical and chemical perspectives, including the main physical principle, refractive index matching via various chemical approaches, such as dissociation of collagen, delipidation, decalcification, dehydration, and hyperhydration, to reduce scattering, as well as decolorization to reduce absorption.
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Affiliation(s)
- Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jingtan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dongyu Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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Avilov SV. Navigating across multi-dimensional space of tissue clearing parameters. Methods Appl Fluoresc 2021; 9:022001. [PMID: 33592593 DOI: 10.1088/2050-6120/abe6fb] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Optical tissue clearing refers to physico-chemical treatments which make thick biological samples transparent by removal of refractive index gradients and light absorbing substances. Although tissue clearing was first reported in 1914, it was not widely used in light microscopy until 21th century, because instrumentation of that time did not permit to acquire and handle images of thick (mm to cm) samples as whole. Rapid progress in optical instrumentation, computers and software over the last decades made micrograph acquisition of centimeter-thick samples feasible. This boosted tissue clearing use and development. Numerous diverse protocols have been developed. They use organic solvents or water-miscible substances, such as detergents and chaotropic agents; some protocols require application of electric field or perfusion with special devices. There is no 'best-for-all' tissue clearing method. Depending on the case, one or another protocol is more suitable. Most of protocols require days or even weeks to complete, thus choosing an unsuitable protocol may cause an important waste of time. Several inter-dependent parameters should be taken into account to choose a tissue clearing protocol, such as: (1) required image quality (resolution, contrast, signal to noise ratio etc), (2) nature and size of the sample, (3) type of labels, (4) characteristics of the available instrumentation, (5) budget, (6) time budget, and (7) feasibility. Present review focusses on the practical aspects of various tissue clearing techniques. It is aimed to help non-experts to choose tissue clearing techniques which are optimal for their particular cases.
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Affiliation(s)
- Sergiy V Avilov
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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46
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Molbay M, Kolabas ZI, Todorov MI, Ohn T, Ertürk A. A guidebook for DISCO tissue clearing. Mol Syst Biol 2021; 17:e9807. [PMID: 33769689 PMCID: PMC7995442 DOI: 10.15252/msb.20209807] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/29/2020] [Accepted: 01/14/2021] [Indexed: 12/14/2022] Open
Abstract
Histological analysis of biological tissues by mechanical sectioning is significantly time-consuming and error-prone due to loss of important information during sample slicing. In the recent years, the development of tissue clearing methods overcame several of these limitations and allowed exploring intact biological specimens by rendering tissues transparent and subsequently imaging them by laser scanning fluorescence microscopy. In this review, we provide a guide for scientists who would like to perform a clearing protocol from scratch without any prior knowledge, with an emphasis on DISCO clearing protocols, which have been widely used not only due to their robustness, but also owing to their relatively straightforward application. We discuss diverse tissue-clearing options and propose solutions for several possible pitfalls. Moreover, after surveying more than 30 researchers that employ tissue clearing techniques in their laboratories, we compiled the most frequently encountered issues and propose solutions. Overall, this review offers an informative and detailed guide through the growing literature of tissue clearing and can help with finding the easiest way for hands-on implementation.
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Affiliation(s)
- Muge Molbay
- Institute for Tissue Engineering and Regenerative Medicine (iTERM)Helmholtz CenterNeuherberg, MunichGermany
- Institute for Stroke and Dementia ResearchKlinikum der Universität MünchenLudwig‐Maximilians‐University MunichMunichGermany
- Munich Medical Research School (MMRS)MunichGermany
| | - Zeynep Ilgin Kolabas
- Institute for Tissue Engineering and Regenerative Medicine (iTERM)Helmholtz CenterNeuherberg, MunichGermany
- Institute for Stroke and Dementia ResearchKlinikum der Universität MünchenLudwig‐Maximilians‐University MunichMunichGermany
- Graduate School for Systemic Neurosciences (GSN)MunichGermany
| | - Mihail Ivilinov Todorov
- Institute for Tissue Engineering and Regenerative Medicine (iTERM)Helmholtz CenterNeuherberg, MunichGermany
- Institute for Stroke and Dementia ResearchKlinikum der Universität MünchenLudwig‐Maximilians‐University MunichMunichGermany
- Graduate School for Systemic Neurosciences (GSN)MunichGermany
| | - Tzu‐Lun Ohn
- Institute for Tissue Engineering and Regenerative Medicine (iTERM)Helmholtz CenterNeuherberg, MunichGermany
- Institute for Stroke and Dementia ResearchKlinikum der Universität MünchenLudwig‐Maximilians‐University MunichMunichGermany
| | - Ali Ertürk
- Institute for Tissue Engineering and Regenerative Medicine (iTERM)Helmholtz CenterNeuherberg, MunichGermany
- Institute for Stroke and Dementia ResearchKlinikum der Universität MünchenLudwig‐Maximilians‐University MunichMunichGermany
- Munich Cluster for Systems Neurology (SyNergy)MunichGermany
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47
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Balestrini A, Joseph V, Dourado M, Reese RM, Shields SD, Rougé L, Bravo DD, Chernov-Rogan T, Austin CD, Chen H, Wang L, Villemure E, Shore DGM, Verma VA, Hu B, Chen Y, Leong L, Bjornson C, Hötzel K, Gogineni A, Lee WP, Suto E, Wu X, Liu J, Zhang J, Gandham V, Wang J, Payandeh J, Ciferri C, Estevez A, Arthur CP, Kortmann J, Wong RL, Heredia JE, Doerr J, Jung M, Vander Heiden JA, Roose-Girma M, Tam L, Barck KH, Carano RAD, Ding HT, Brillantes B, Tam C, Yang X, Gao SS, Ly JQ, Liu L, Chen L, Liederer BM, Lin JH, Magnuson S, Chen J, Hackos DH, Elstrott J, Rohou A, Safina BS, Volgraf M, Bauer RN, Riol-Blanco L. A TRPA1 inhibitor suppresses neurogenic inflammation and airway contraction for asthma treatment. J Exp Med 2021; 218:211821. [PMID: 33620419 PMCID: PMC7918756 DOI: 10.1084/jem.20201637] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/19/2020] [Accepted: 12/23/2020] [Indexed: 12/31/2022] Open
Abstract
Despite the development of effective therapies, a substantial proportion of asthmatics continue to have uncontrolled symptoms, airflow limitation, and exacerbations. Transient receptor potential cation channel member A1 (TRPA1) agonists are elevated in human asthmatic airways, and in rodents, TRPA1 is involved in the induction of airway inflammation and hyperreactivity. Here, the discovery and early clinical development of GDC-0334, a highly potent, selective, and orally bioavailable TRPA1 antagonist, is described. GDC-0334 inhibited TRPA1 function on airway smooth muscle and sensory neurons, decreasing edema, dermal blood flow (DBF), cough, and allergic airway inflammation in several preclinical species. In a healthy volunteer Phase 1 study, treatment with GDC-0334 reduced TRPA1 agonist-induced DBF, pain, and itch, demonstrating GDC-0334 target engagement in humans. These data provide therapeutic rationale for evaluating TRPA1 inhibition as a clinical therapy for asthma.
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Affiliation(s)
- Alessia Balestrini
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA
| | - Victory Joseph
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA
| | - Michelle Dourado
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA
| | - Rebecca M Reese
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA
| | - Shannon D Shields
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA
| | - Lionel Rougé
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA
| | - Daniel D Bravo
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, CA
| | - Tania Chernov-Rogan
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, CA
| | - Cary D Austin
- Department of Pathology, Genentech, Inc., South San Francisco, CA
| | - Huifen Chen
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Lan Wang
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Elisia Villemure
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Daniel G M Shore
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Vishal A Verma
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Baihua Hu
- Pharmaron-Beijing Co. Ltd., BDA, Beijing, People's Republic of China
| | - Yong Chen
- Pharmaron-Beijing Co. Ltd., BDA, Beijing, People's Republic of China
| | - Laurie Leong
- Department of Pathology, Genentech, Inc., South San Francisco, CA
| | - Chris Bjornson
- Department of Pathology, Genentech, Inc., South San Francisco, CA
| | - Kathy Hötzel
- Department of Pathology, Genentech, Inc., South San Francisco, CA
| | - Alvin Gogineni
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA
| | - Eric Suto
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA
| | - Xiumin Wu
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA
| | - John Liu
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA
| | - Juan Zhang
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA
| | - Vineela Gandham
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA
| | - Jianyong Wang
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, CA
| | - Jian Payandeh
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA
| | - Claudio Ciferri
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA
| | - Alberto Estevez
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA
| | | | - Jens Kortmann
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA
| | - Ryan L Wong
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA
| | - Jose E Heredia
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA
| | - Jonas Doerr
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
| | - Min Jung
- Department of OMNI Bioinformatics, Genentech, Inc., South San Francisco, CA
| | | | - Merone Roose-Girma
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
| | - Lucinda Tam
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
| | - Kai H Barck
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA
| | - Richard A D Carano
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA
| | - Han Ting Ding
- Department of Clinical Pharmacology, Genentech, Inc., South San Francisco, CA
| | - Bobby Brillantes
- Department of Biomolecular Resources, Genentech, Inc., South San Francisco, CA
| | - Christine Tam
- Department of Biomolecular Resources, Genentech, Inc., South San Francisco, CA
| | - Xiaoying Yang
- Department of Product Development Biometric Biostatistics, Genentech, Inc., South San Francisco, CA
| | - Simon S Gao
- Department of Clinical Imaging, Genentech, Inc., South San Francisco, CA
| | - Justin Q Ly
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA
| | - Liling Liu
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA
| | - Liuxi Chen
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA
| | - Bianca M Liederer
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA
| | - Joseph H Lin
- Department of Early Clinical Development, Genentech, Inc., South San Francisco, CA
| | - Steven Magnuson
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Jun Chen
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, CA
| | - David H Hackos
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA
| | - Justin Elstrott
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA
| | - Alexis Rohou
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA
| | - Brian S Safina
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Matthew Volgraf
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Rebecca N Bauer
- Department of OMNI-Biomarker Development, Genentech, Inc., South San Francisco, CA
| | - Lorena Riol-Blanco
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA
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48
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Rybin MJ, Ivan ME, Ayad NG, Zeier Z. Organoid Models of Glioblastoma and Their Role in Drug Discovery. Front Cell Neurosci 2021; 15:605255. [PMID: 33613198 PMCID: PMC7892608 DOI: 10.3389/fncel.2021.605255] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma (GBM) is a devastating adult brain cancer with high rates of recurrence and treatment resistance. Cellular heterogeneity and extensive invasion of surrounding brain tissues are characteristic features of GBM that contribute to its intractability. Current GBM model systems do not recapitulate some of the complex features of GBM and have not produced sufficiently-effective treatments. This has cast doubt on the effectiveness of current GBM models and drug discovery paradigms. In search of alternative pre-clinical GBM models, various 3D organoid-based GBM model systems have been developed using human cells. The scalability of these systems and potential to more accurately model characteristic features of GBM, provide promising new avenues for pre-clinical GBM research and drug discovery efforts. Here, we review the current suite of organoid-GBM models, their individual strengths and weaknesses, and discuss their future applications with an emphasis on compound screening.
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Affiliation(s)
- Matthew J. Rybin
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, United States
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Michael E. Ivan
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Nagi G. Ayad
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Zane Zeier
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, United States
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
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49
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Wang X, Zeng W, Yang X, Zhang Y, Fang C, Zeng S, Han Y, Fei P. Bi-channel image registration and deep-learning segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain. eLife 2021; 10:e63455. [PMID: 33459255 PMCID: PMC7840180 DOI: 10.7554/elife.63455] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/27/2020] [Indexed: 12/21/2022] Open
Abstract
We have developed an open-source software called bi-channel image registration and deep-learning segmentation (BIRDS) for the mapping and analysis of 3D microscopy data and applied this to the mouse brain. The BIRDS pipeline includes image preprocessing, bi-channel registration, automatic annotation, creation of a 3D digital frame, high-resolution visualization, and expandable quantitative analysis. This new bi-channel registration algorithm is adaptive to various types of whole-brain data from different microscopy platforms and shows dramatically improved registration accuracy. Additionally, as this platform combines registration with neural networks, its improved function relative to the other platforms lies in the fact that the registration procedure can readily provide training data for network construction, while the trained neural network can efficiently segment-incomplete/defective brain data that is otherwise difficult to register. Our software is thus optimized to enable either minute-timescale registration-based segmentation of cross-modality, whole-brain datasets or real-time inference-based image segmentation of various brain regions of interest. Jobs can be easily submitted and implemented via a Fiji plugin that can be adapted to most computing environments.
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Affiliation(s)
- Xuechun Wang
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and TechnologyWuhanChina
| | - Weilin Zeng
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and TechnologyWuhanChina
| | - Xiaodan Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Yongsheng Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and TechnologyWuhanChina
| | - Chunyu Fang
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and TechnologyWuhanChina
| | - Shaoqun Zeng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and TechnologyWuhanChina
| | - Yunyun Han
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Peng Fei
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and TechnologyWuhanChina
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50
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Abstract
Although the inflammatory cytokine IL-10 is pivotal in regulatory B-cell function, detecting IL-10-producing B cells by intracellular IL-10 staining requires multiple steps and tedious preparation. In contrast, the Il10-eGFP reporter mouse model (VertX), generated in 2009, allows easier and quicker detection of IL-10-producing B cells with the possibility of sorting viable cells without membrane permeabilization and ex vivo activation. Even though detecting IL-10+ cells is simpler, several nuances are important. For example, methanol-containing buffers delete GFP signal, while long-term fixation can maintain GFP intensity but decreases other intracellular signals (FOXP3, etc.). Here, we provide optimized and improved protocols for GFP detection in intestinal B cells and isolation techniques of lamina propria, spleen, mesenteric lymph node, peritoneum, and blood cells from VertX mice.
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Affiliation(s)
- Akihiko Oka
- Center for Gastrointestinal Biology and Disease, Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Internal Medicine II, Shimane University Faculty of Medicine, Izumo, Shimane, Japan
| | - Bo Liu
- Center for Gastrointestinal Biology and Disease, Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeremy W Herzog
- Center for Gastrointestinal Biology and Disease, Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- National Gnotobiotic Rodent Resource Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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