1
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Rallapalli H, McCall EC, Koretsky AP. Genetic control of MRI contrast using the manganese transporter Zip14. Magn Reson Med 2024; 92:820-835. [PMID: 38573932 PMCID: PMC11142883 DOI: 10.1002/mrm.29993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/15/2023] [Accepted: 12/12/2023] [Indexed: 04/06/2024]
Abstract
PURPOSE Gene-expression reporter systems, such as green fluorescent protein, have been instrumental to understanding biological processes in living organisms at organ system, tissue, cell, and molecular scales. More than 30 years of work on developing MRI-visible gene-expression reporter systems has resulted in a variety of clever application-specific methods. However, these techniques have not yet been widely adopted, so a general-purpose expression reporter is still required. Here, we demonstrate that the manganese ion transporter Zip14 is an in vivo MRI-visible, flexible, and robust gene-expression reporter to meet this need. METHODS Plasmid constructs consisting of a cell type-specific promoter, gene coding for human Zip14, and a histology-visible tag were packaged into adeno-associated viruses. These viruses were intracranially injected into the mouse brain. Serial in vivo MRI was performed using a vendor-supplied 3D-MPRAGE sequence. No additional contrast agents were administered. Animals were sacrificed after the last imaging timepoint for immunohistological validation. RESULTS Neuron-specific overexpression of Zip14 produced substantial and long-lasting changes in MRI contrast. Using appropriate viruses enabled both anterograde and retrograde neural tracing. Expression of Zip14 in astrocytes also enabled MRI of glia populations in the living mammalian brain. CONCLUSIONS The flexibility of this system as an MRI-visible gene-expression reporter will enable many applications of serial, high-resolution imaging of gene expression for basic science and therapy development.
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Affiliation(s)
- Harikrishna Rallapalli
- Section on Plasticity and Imaging of the Nervous System, NINDS/NIH, Bethesda, Maryland, USA
| | - Eleanor C McCall
- Section on Plasticity and Imaging of the Nervous System, NINDS/NIH, Bethesda, Maryland, USA
| | - Alan P Koretsky
- Section on Plasticity and Imaging of the Nervous System, NINDS/NIH, Bethesda, Maryland, USA
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2
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Ding Y, Huang Y, Gao P, Thai A, Chilaparasetti AN, Gopi M, Xu X, Li C. Brain image data processing using collaborative data workflows on Texera. Front Neural Circuits 2024; 18:1398884. [PMID: 39050044 PMCID: PMC11266044 DOI: 10.3389/fncir.2024.1398884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/20/2024] [Indexed: 07/27/2024] Open
Abstract
In the realm of neuroscience, mapping the three-dimensional (3D) neural circuitry and architecture of the brain is important for advancing our understanding of neural circuit organization and function. This study presents a novel pipeline that transforms mouse brain samples into detailed 3D brain models using a collaborative data analytics platform called "Texera." The user-friendly Texera platform allows for effective interdisciplinary collaboration between team members in neuroscience, computer vision, and data processing. Our pipeline utilizes the tile images from a serial two-photon tomography/TissueCyte system, then stitches tile images into brain section images, and constructs 3D whole-brain image datasets. The resulting 3D data supports downstream analyses, including 3D whole-brain registration, atlas-based segmentation, cell counting, and high-resolution volumetric visualization. Using this platform, we implemented specialized optimization methods and obtained significant performance enhancement in workflow operations. We expect the neuroscience community can adopt our approach for large-scale image-based data processing and analysis.
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Affiliation(s)
- Yunyan Ding
- Department of Computer Science, University of California, Irvine, Irvine, CA, United States
| | - Yicong Huang
- Department of Computer Science, University of California, Irvine, Irvine, CA, United States
| | - Pan Gao
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Andy Thai
- Department of Computer Science, University of California, Irvine, Irvine, CA, United States
| | | | - M. Gopi
- Department of Computer Science, University of California, Irvine, Irvine, CA, United States
| | - Xiangmin Xu
- Department of Computer Science, University of California, Irvine, Irvine, CA, United States
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- The Center for Neural Circuit Mapping, University of California, Irvine, Irvine, CA, United States
| | - Chen Li
- Department of Computer Science, University of California, Irvine, Irvine, CA, United States
- The Center for Neural Circuit Mapping, University of California, Irvine, Irvine, CA, United States
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3
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Feng R, Xie J, Gao L. EDTP enhances and protects the fluorescent signal of GFP in cleared and expanded tissues. Sci Rep 2024; 14:15279. [PMID: 38961181 PMCID: PMC11222453 DOI: 10.1038/s41598-024-66398-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024] Open
Abstract
Advanced 3D high-resolution imaging techniques are essential for investigating biological challenges, such as neural circuit analysis and tumor microenvironment in intact tissues. However, the fluorescence signal emitted by endogenous fluorescent proteins in cleared or expanded biological samples gradually diminishes with repeated irradiation and prolonged imaging, compromising its ability to accurately depict the underlying scientific problem. We have developed a strategy to preserve fluorescence in cleared and expanded tissue samples during prolonged high-resolution three-dimensional imaging. We evaluated various compounds at different concentrations to determine their ability to enhance fluorescence intensity and resistance to photobleaching while maintaining the structural integrity of the tissue. Specifically, we investigated the impact of EDTP utilization on GFP, as it has been observed to significantly improve fluorescence intensity, resistance to photobleaching, and maintain fluorescence during extended room temperature storage. This breakthrough will facilitate extended hydrophilic and hydrogel-based clearing and expansion methods for achieving long-term high-resolution 3D imaging of cleared biological tissues by effectively safeguarding fluorescent proteins within the tissue.
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Affiliation(s)
- Ruili Feng
- Fudan University, Shanghai, 200433, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China.
| | - Jiongfang Xie
- Fudan University, Shanghai, 200433, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China
| | - Liang Gao
- Fudan University, Shanghai, 200433, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China
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4
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Otomo K, Omura T, Nozawa Y, Edwards SJ, Sato Y, Saito Y, Yagishita S, Uchida H, Watakabe Y, Naitou K, Yanai R, Sahara N, Takagi S, Katayama R, Iwata Y, Shiokawa T, Hayakawa Y, Otsuka K, Watanabe-Takano H, Haneda Y, Fukuhara S, Fujiwara M, Nii T, Meno C, Takeshita N, Yashiro K, Rosales Rocabado JM, Kaku M, Yamada T, Oishi Y, Koike H, Cheng Y, Sekine K, Koga JI, Sugiyama K, Kimura K, Karube F, Kim H, Manabe I, Nemoto T, Tainaka K, Hamada A, Brismar H, Susaki EA. descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques. Nat Commun 2024; 15:4941. [PMID: 38866781 PMCID: PMC11169475 DOI: 10.1038/s41467-024-49131-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Despite widespread adoption of tissue clearing techniques in recent years, poor access to suitable light-sheet fluorescence microscopes remains a major obstacle for biomedical end-users. Here, we present descSPIM (desktop-equipped SPIM for cleared specimens), a low-cost ($20,000-50,000), low-expertise (one-day installation by a non-expert), yet practical do-it-yourself light-sheet microscope as a solution for this bottleneck. Even the most fundamental configuration of descSPIM enables multi-color imaging of whole mouse brains and a cancer cell line-derived xenograft tumor mass for the visualization of neurocircuitry, assessment of drug distribution, and pathological examination by false-colored hematoxylin and eosin staining in a three-dimensional manner. Academically open-sourced ( https://github.com/dbsb-juntendo/descSPIM ), descSPIM allows routine three-dimensional imaging of cleared samples in minutes. Thus, the dissemination of descSPIM will accelerate biomedical discoveries driven by tissue clearing technologies.
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Affiliation(s)
- Kohei Otomo
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Takaki Omura
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Neurosurgery, University of Tokyo, Tokyo, Japan
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuki Nozawa
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan
| | - Steven J Edwards
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yukihiko Sato
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuri Saito
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shigehiro Yagishita
- Department of Pharmacology and Therapeutics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hitoshi Uchida
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yuki Watakabe
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kiyotada Naitou
- Department of Basic Veterinary Science, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Rin Yanai
- Advanced Neuroimaging Center, Institute for Quantum Medical Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Naruhiko Sahara
- Advanced Neuroimaging Center, Institute for Quantum Medical Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Satoshi Takagi
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yusuke Iwata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshiro Shiokawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kensuke Otsuka
- Biology and Environmental Chemistry Division, Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry, Chiba, Japan
| | - Haruko Watanabe-Takano
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Yuka Haneda
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Shigetomo Fukuhara
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Miku Fujiwara
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takenobu Nii
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Chikara Meno
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naoki Takeshita
- Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kenta Yashiro
- Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Juan Marcelo Rosales Rocabado
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masaru Kaku
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Tatsuya Yamada
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Yumiko Oishi
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Koike
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yinglan Cheng
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keisuke Sekine
- Laboratory of Cancer Cell Systems, National Cancer Center Research Institute, Tokyo, Japan
| | - Jun-Ichiro Koga
- The Second Department of Internal Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Kaori Sugiyama
- Institute for Advanced Research of Biosystem Dynamics, Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Kenichi Kimura
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | - Fuyuki Karube
- Lab of Histology and Cytology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Hyeree Kim
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ichiro Manabe
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomomi Nemoto
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akinobu Hamada
- Department of Pharmacology and Therapeutics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Etsuo A Susaki
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan.
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan.
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan.
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5
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Barr J, Walz A, Restaino AC, Amit M, Barclay SM, Vichaya EG, Spanos WC, Dantzer R, Talbot S, Vermeer PD. Tumor-infiltrating nerves functionally alter brain circuits and modulate behavior in a male mouse model of head-and-neck cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.18.562990. [PMID: 37905135 PMCID: PMC10614955 DOI: 10.1101/2023.10.18.562990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Cancer patients often experience changes in mental health, prompting an exploration into whether nerves infiltrating tumors contribute to these alterations by impacting brain functions. Using a male mouse model for head and neck cancer, we utilized neuronal tracing techniques and show that tumor-infiltrating nerves indeed connect to distinct brain areas via the ipsilateral trigeminal ganglion. The activation of this neuronal circuitry led to behavioral alterations represented by decreased nest-building, increased latency to eat a cookie, and reduced wheel running. Tumor-infiltrating nociceptor neurons exhibited heightened activity, as indicated by increased calcium mobilization. Correspondingly, the specific brain regions receiving these neural projections showed elevated cFos and delta FosB expression in tumor-bearing mice, alongside markedly intensified calcium responses compared to non-tumor-bearing counterparts. The genetic elimination of nociceptor neurons in tumor-bearing mice led to decreased brain Fos expression and mitigated the behavioral alterations induced by the presence of the tumor. While analgesic treatment successfully restored behaviors involving oral movements to normalcy in tumor-bearing mice, it did not have a similar therapeutic effect on voluntary wheel running. This discrepancy points towards an intricate relationship, where pain is not the exclusive driver of such behavioral shifts. Unraveling the interaction between the tumor, infiltrating nerves, and the brain is pivotal to developing targeted interventions to alleviate the mental health burdens associated with cancer.
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Mino T, Nonaka H, Hamachi I. Molecular anchoring and fluorescent labeling in animals compatible with tissue clearing for 3D imaging. Curr Opin Chem Biol 2024; 81:102474. [PMID: 38838505 DOI: 10.1016/j.cbpa.2024.102474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024]
Abstract
Analyzing the quantity and distribution of molecules throughout intact biological tissue is crucial for understanding various biological phenomena. Traditional methods involving destructive extraction result in the loss of spatial information. Conversely, tissue-clearing techniques combined with fluorescence imaging have recently emerged as a powerful tool for deep tissue imaging without sacrificing spatial coverage. Key to this approach is the anchoring and labeling of targets in intact tissue. In this review, methods for anchoring and labeling proteins, lipids, carbohydrates, and small molecules are presented. Future directions include the development of activity-based probes that work in vivo and mark transient events with spatial information to enable a deeper understanding of biological phenomena.
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Affiliation(s)
- Takeharu Mino
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hiroshi Nonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan.
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7
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Choi YK, Feng L, Jeong WK, Kim J. Connecto-informatics at the mesoscale: current advances in image processing and analysis for mapping the brain connectivity. Brain Inform 2024; 11:15. [PMID: 38833195 DOI: 10.1186/s40708-024-00228-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/08/2024] [Indexed: 06/06/2024] Open
Abstract
Mapping neural connections within the brain has been a fundamental goal in neuroscience to understand better its functions and changes that follow aging and diseases. Developments in imaging technology, such as microscopy and labeling tools, have allowed researchers to visualize this connectivity through high-resolution brain-wide imaging. With this, image processing and analysis have become more crucial. However, despite the wealth of neural images generated, access to an integrated image processing and analysis pipeline to process these data is challenging due to scattered information on available tools and methods. To map the neural connections, registration to atlases and feature extraction through segmentation and signal detection are necessary. In this review, our goal is to provide an updated overview of recent advances in these image-processing methods, with a particular focus on fluorescent images of the mouse brain. Our goal is to outline a pathway toward an integrated image-processing pipeline tailored for connecto-informatics. An integrated workflow of these image processing will facilitate researchers' approach to mapping brain connectivity to better understand complex brain networks and their underlying brain functions. By highlighting the image-processing tools available for fluroscent imaging of the mouse brain, this review will contribute to a deeper grasp of connecto-informatics, paving the way for better comprehension of brain connectivity and its implications.
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Affiliation(s)
- Yoon Kyoung Choi
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | | | - Won-Ki Jeong
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | - Jinhyun Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea.
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea.
- KIST-SKKU Brain Research Center, SKKU Institute for Convergence, Sungkyunkwan University, Suwon, South Korea.
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8
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Kim KW. Clearing techniques for deeper imaging of plants and plant-microbe interactions. Appl Microsc 2024; 54:5. [PMID: 38816666 PMCID: PMC11139840 DOI: 10.1186/s42649-024-00098-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
Plant cells are uniquely characterized by exhibiting cell walls, pigments, and phenolic compounds, which can impede microscopic observations by absorbing and scattering light. The concept of clearing was first proposed in the late nineteenth century to address this issue, aiming to render plant specimens transparent using chloral hydrate. Clearing techniques involve chemical procedures that render biological specimens transparent, enabling deep imaging without physical sectioning. Drawing inspiration from clearing techniques for animal specimens, various protocols have been adapted for plant research. These procedures include (i) hydrophobic methods (e.g., Visikol™), (ii) hydrophilic methods (ScaleP and ClearSee), and (iii) hydrogel-based methods (PEA-CLARITY). Initially, clearing techniques for plants were mainly utilized for deep imaging of seeds and leaves of herbaceous plants such as Arabidopsis thaliana and rice. Utilizing cell wall-specific fluorescent dyes for plants and fungi, researchers have documented the post-penetration behavior of plant pathogenic fungi within hosts. State-of-the-art plant clearing techniques, coupled with microbe-specific labeling and high-throughput imaging methods, offer the potential to advance the in planta characterization of plant microbiomes.
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Affiliation(s)
- Ki Woo Kim
- Department of Forest Ecology and Protection, Tree Diagnostic Center, Kyungpook National University, Sangju, 37224, Republic of Korea.
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9
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Mori D, Inami C, Ikeda R, Sawahata M, Urata S, Yamaguchi ST, Kobayashi Y, Fujita K, Arioka Y, Okumura H, Kushima I, Kodama A, Suzuki T, Hirao T, Yoshimi A, Sobue A, Ito T, Noda Y, Mizoguchi H, Nagai T, Kaibuchi K, Okabe S, Nishiguchi K, Kume K, Yamada K, Ozaki N. Mice with deficiency in Pcdh15, a gene associated with bipolar disorders, exhibit significantly elevated diurnal amplitudes of locomotion and body temperature. Transl Psychiatry 2024; 14:216. [PMID: 38806495 PMCID: PMC11133426 DOI: 10.1038/s41398-024-02952-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024] Open
Abstract
Genetic factors significantly affect the pathogenesis of psychiatric disorders. However, the specific pathogenic mechanisms underlying these effects are not fully understood. Recent extensive genomic studies have implicated the protocadherin-related 15 (PCDH15) gene in the onset of psychiatric disorders, such as bipolar disorder (BD). To further investigate the pathogenesis of these psychiatric disorders, we developed a mouse model lacking Pcdh15. Notably, although PCDH15 is primarily identified as the causative gene of Usher syndrome, which presents with visual and auditory impairments, our mice with Pcdh15 homozygous deletion (Pcdh15-null) did not exhibit observable structural abnormalities in either the retina or the inner ear. The Pcdh15-null mice showed very high levels of spontaneous motor activity which was too disturbed to perform standard behavioral testing. However, the Pcdh15 heterozygous deletion mice (Pcdh15-het) exhibited enhanced spontaneous locomotor activity, reduced prepulse inhibition, and diminished cliff avoidance behavior. These observations agreed with the symptoms observed in patients with various psychiatric disorders and several mouse models of psychiatric diseases. Specifically, the hyperactivity may mirror the manic episodes in BD. To obtain a more physiological, long-term quantification of the hyperactive phenotype, we implanted nano tag® sensor chips in the animals, to enable the continuous monitoring of both activity and body temperature. During the light-off period, Pcdh15-null exhibited elevated activity and body temperature compared with wild-type (WT) mice. However, we observed a decreased body temperature during the light-on period. Comprehensive brain activity was visualized using c-Fos mapping, which was assessed during the activity and temperature peak and trough. There was a stark contrast between the distribution of c-Fos expression in Pcdh15-null and WT brains during both the light-on and light-off periods. These results provide valuable insights into the neural basis of the behavioral and thermal characteristics of Pcdh15-deletion mice. Therefore, Pcdh15-deletion mice can be a novel model for BD with mania and other psychiatric disorders, with a strong genetic component that satisfies both construct and surface validity.
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Affiliation(s)
- Daisuke Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.
- Brain and Mind Research Center, Nagoya University, Nagoya, Aichi, Japan.
- Department of Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.
| | - Chihiro Inami
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University, Graduate School of Medicine, Nagoya, Aichi, Japan
- Department of Neuropharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Ryosuke Ikeda
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahito Sawahata
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University, Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Shinji Urata
- Department of Otolaryngology, Graduate School of Medicine, The University of Tokyo, Tokyo Pref., Japan
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo Pref., Japan
| | - Sho T Yamaguchi
- Department of Neuropharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | | | - Kosuke Fujita
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yuko Arioka
- Department of Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Hiroki Okumura
- Department of Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University, Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Akiko Kodama
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Toshiaki Suzuki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Hirao
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akira Yoshimi
- Division of Clinical Sciences and Neuropsychopharmacology, Meijo University Faculty of Pharmacy, Nagoya, Aichi, Japan
| | - Akira Sobue
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University, Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Takahiro Ito
- Division of Clinical Sciences and Neuropsychopharmacology, Meijo University Faculty of Pharmacy, Nagoya, Aichi, Japan
| | - Yukikiro Noda
- Division of Clinical Sciences and Neuropsychopharmacology, Meijo University Faculty of Pharmacy, Nagoya, Aichi, Japan
| | - Hiroyuki Mizoguchi
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University, Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Taku Nagai
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University, Graduate School of Medicine, Nagoya, Aichi, Japan
- Division of Behavioral Neuropharmacology, International Center for Brain Science (ICBS), Fujita Health University, Toyoake, Aichi, Japan
| | - Kozo Kaibuchi
- Division of Cell Biology, International Center for Brain Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo Pref., Japan
| | - Koji Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kazuhiko Kume
- Department of Neuropharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Kiyofumi Yamada
- Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University, Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Norio Ozaki
- Department of Pathophysiology of Mental Disorders, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi, Japan
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10
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Chen Y, Yang H, Luo Y, Niu Y, Yu M, Deng S, Wang X, Deng H, Chen H, Gao L, Li X, Xu P, Xue F, Miao J, Shi SH, Zhong Y, Ma C, Lei B. Photoacoustic Tomography with Temporal Encoding Reconstruction (PATTERN) for cross-modal individual analysis of the whole brain. Nat Commun 2024; 15:4228. [PMID: 38762498 PMCID: PMC11102525 DOI: 10.1038/s41467-024-48393-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 04/26/2024] [Indexed: 05/20/2024] Open
Abstract
Cross-modal analysis of the same whole brain is an ideal strategy to uncover brain function and dysfunction. However, it remains challenging due to the slow speed and destructiveness of traditional whole-brain optical imaging techniques. Here we develop a new platform, termed Photoacoustic Tomography with Temporal Encoding Reconstruction (PATTERN), for non-destructive, high-speed, 3D imaging of ex vivo rodent, ferret, and non-human primate brains. Using an optimally designed image acquisition scheme and an accompanying machine-learning algorithm, PATTERN extracts signals of genetically-encoded probes from photobleaching-based temporal modulation and enables reliable visualization of neural projection in the whole central nervous system with 3D isotropic resolution. Without structural and biological perturbation to the sample, PATTERN can be combined with other whole-brain imaging modalities to acquire the whole-brain image with both high resolution and morphological fidelity. Furthermore, cross-modal transcriptome analysis of an individual brain is achieved by PATTERN imaging. Together, PATTERN provides a compatible and versatile strategy for brain-wide cross-modal analysis at the individual level.
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Affiliation(s)
- Yuwen Chen
- Department of Electronic Engineering, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, PR China
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, 100084, PR China
| | - Haoyu Yang
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China
- IDG/McGovern Institute of Brain Research, Beijing, 100084, PR China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Yan Luo
- Department of Electronic Engineering, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, PR China
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, 100084, PR China
| | - Yijun Niu
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China
- IDG/McGovern Institute of Brain Research, Beijing, 100084, PR China
| | - Muzhou Yu
- School of Computer Science, Xi'an Jiaotong University, Xi'an, 713599, PR China
| | - Shanjun Deng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Xuanhao Wang
- Research Center for Humanoid Sensing, Zhejiang Laboratory, Hangzhou, 311100, PR China
| | - Handi Deng
- Department of Electronic Engineering, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, PR China
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, 100084, PR China
| | - Haichao Chen
- School of Medicine, Tsinghua University, Beijing, 100084, PR China
| | - Lixia Gao
- Department of Neurology of the Second Affiliated Hospital and Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Zhejiang University, Hangzhou, 310029, PR China
| | - Xinjian Li
- Department of Neurology of the Second Affiliated Hospital and Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Zhejiang University, Hangzhou, 310029, PR China
| | - Pingyong Xu
- Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Fudong Xue
- Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Jing Miao
- Canterbury School, New Milford, CT, 06776, USA
| | - Song-Hai Shi
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China
- IDG/McGovern Institute of Brain Research, Beijing, 100084, PR China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Yi Zhong
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China
- IDG/McGovern Institute of Brain Research, Beijing, 100084, PR China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Cheng Ma
- Department of Electronic Engineering, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, PR China.
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, 100084, PR China.
| | - Bo Lei
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China.
- IDG/McGovern Institute of Brain Research, Beijing, 100084, PR China.
- Beijing Academy of Artificial Intelligence, Beijing, 100084, PR China.
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11
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Yu T, Yang Q, Peng B, Gu Z, Zhu D. Vascularized organoid-on-a-chip: design, imaging, and analysis. Angiogenesis 2024; 27:147-172. [PMID: 38409567 DOI: 10.1007/s10456-024-09905-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/11/2024] [Indexed: 02/28/2024]
Abstract
Vascularized organoid-on-a-chip (VOoC) models achieve substance exchange in deep layers of organoids and provide a more physiologically relevant system in vitro. Common designs for VOoC primarily involve two categories: self-assembly of endothelial cells (ECs) to form microvessels and pre-patterned vessel lumens, both of which include the hydrogel region for EC growth and allow for controlled fluid perfusion on the chip. Characterizing the vasculature of VOoC often relies on high-resolution microscopic imaging. However, the high scattering of turbid tissues can limit optical imaging depth. To overcome this limitation, tissue optical clearing (TOC) techniques have emerged, allowing for 3D visualization of VOoC in conjunction with optical imaging techniques. The acquisition of large-scale imaging data, coupled with high-resolution imaging in whole-mount preparations, necessitates the development of highly efficient analysis methods. In this review, we provide an overview of the chip designs and culturing strategies employed for VOoC, as well as the applicable optical imaging and TOC methods. Furthermore, we summarize the vascular analysis techniques employed in VOoC, including deep learning. Finally, we discuss the existing challenges in VOoC and vascular analysis methods and provide an outlook for future development.
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Affiliation(s)
- Tingting Yu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
- Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Qihang Yang
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
- Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, Xi'an, Shanxi, 710072, China
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China
- Institute of Biomaterials and Medical Devices, Southeast University, Suzhou, Jiangsu, 215163, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
- Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
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12
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Takahashi-Yamashiro K, Miyazono K. Tissue clearing method in visualization of cancer progression and metastasis. Ups J Med Sci 2024; 129:10634. [PMID: 38716075 PMCID: PMC11075440 DOI: 10.48101/ujms.v129.10634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 03/07/2024] [Indexed: 05/24/2024] Open
Abstract
Since various imaging modalities have been developed, cancer metastasis can be detected from an early stage. However, limitations still exist, especially in terms of spatial resolution. Tissue-clearing technology has emerged as a new imaging modality in cancer research, which has been developed and utilized for a long time mainly in neuroscience field. This method enables us to detect cancer metastatic foci with single-cell resolution at whole mouse body/organ level. On top of that, 3D images of cancer metastasis of whole mouse organs make it easy to understand their characteristics. Recently, further applications of tissue clearing methods were reported in combination with reporter systems, labeling, and machine learning. In this review, we would like to provide an overview of this technique and current applications in cancer research and discuss their potentials and limitations.
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Affiliation(s)
- Kei Takahashi-Yamashiro
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton, Alberta, Canada
| | - Kohei Miyazono
- Department of Applied Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Cancer Invasion and Metastasis, Institute for Medical Sciences, RIKEN, Yokohama City, Kanagawa, Japan
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13
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Ziak J, Dorskind JM, Trigg B, Sudarsanam S, Jin XO, Hand RA, Kolodkin AL. Microtubule-binding protein MAP1B regulates interstitial axon branching of cortical neurons via the tubulin tyrosination cycle. EMBO J 2024; 43:1214-1243. [PMID: 38388748 PMCID: PMC10987652 DOI: 10.1038/s44318-024-00050-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/24/2024] Open
Abstract
Regulation of directed axon guidance and branching during development is essential for the generation of neuronal networks. However, the molecular mechanisms that underlie interstitial (or collateral) axon branching in the mammalian brain remain unresolved. Here, we investigate interstitial axon branching in vivo using an approach for precise labeling of layer 2/3 callosal projection neurons (CPNs). This method allows for quantitative analysis of axonal morphology at high acuity and also manipulation of gene expression in well-defined temporal windows. We find that the GSK3β serine/threonine kinase promotes interstitial axon branching in layer 2/3 CPNs by releasing MAP1B-mediated inhibition of axon branching. Further, we find that the tubulin tyrosination cycle is a key downstream component of GSK3β/MAP1B signaling. These data suggest a cell-autonomous molecular regulation of cortical neuron axon morphology, in which GSK3β can release a MAP1B-mediated brake on interstitial axon branching upstream of the posttranslational tubulin code.
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Affiliation(s)
- Jakub Ziak
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD, 21205, USA
| | - Joelle M Dorskind
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD, 21205, USA
- Novartis Institutes for BioMedical Research, Boston, MA, USA
| | - Brian Trigg
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD, 21205, USA
| | - Sriram Sudarsanam
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD, 21205, USA
| | - Xinyu O Jin
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD, 21205, USA
| | - Randal A Hand
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD, 21205, USA
- Prilenia Therapeutics, Boston, MA, USA
| | - Alex L Kolodkin
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD, 21205, USA.
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14
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Vladimirov N, Voigt FF, Naert T, Araujo GR, Cai R, Reuss AM, Zhao S, Schmid P, Hildebrand S, Schaettin M, Groos D, Mateos JM, Bethge P, Yamamoto T, Aerne V, Roebroeck A, Ertürk A, Aguzzi A, Ziegler U, Stoeckli E, Baudis L, Lienkamp SS, Helmchen F. Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for cleared samples. Nat Commun 2024; 15:2679. [PMID: 38538644 PMCID: PMC10973490 DOI: 10.1038/s41467-024-46770-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
In 2015, we launched the mesoSPIM initiative, an open-source project for making light-sheet microscopy of large cleared tissues more accessible. Meanwhile, the demand for imaging larger samples at higher speed and resolution has increased, requiring major improvements in the capabilities of such microscopes. Here, we introduce the next-generation mesoSPIM ("Benchtop") with a significantly increased field of view, improved resolution, higher throughput, more affordable cost, and simpler assembly compared to the original version. We develop an optical method for testing detection objectives that enables us to select objectives optimal for light-sheet imaging with large-sensor cameras. The improved mesoSPIM achieves high spatial resolution (1.5 µm laterally, 3.3 µm axially) across the entire field of view, magnification up to 20×, and supports sample sizes ranging from sub-mm up to several centimeters while being compatible with multiple clearing techniques. The microscope serves a broad range of applications in neuroscience, developmental biology, pathology, and even physics.
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Grants
- U01 NS090475 NINDS NIH HHS
- This work was supported by the University Research Priority Program (URPP) “Adaptive Brain Circuits in Development and Learning (AdaBD)” of the University of Zurich (N.V., E.S. and F.H.). Additionally, F.F.V. is supported by an HFSP fellowship (LT00687), T.N. received funding from H2020 Marie Skłodowska-Curie Actions (xenCAKUT - 891127), A.R. and S.H. were supported by a Dutch Science Foundation VIDI Grant (14637), and A.R. was supported by an ERC Starting Grant (MULTICONNECT, 639938). Further funding support came from the Swiss National Science Foundation (SNF grant nos. 31003B-170269, 310030_192617 and CRSII5-18O316 to F.H., 310030_189102 to S.S.L., 200020_204950 to L.B., G.R.A, and V.A.); from an ERC Starting Grant by the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 804474, DiRECT, S.S.L); and the US Brain Initiative (1U01NS090475-01, F.H.).
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Affiliation(s)
- Nikita Vladimirov
- Brain Research Institute, University of Zurich, Zurich, Switzerland.
- University Research Priority Program (URPP), Adaptive Brain Circuits in Development and Learning, University of Zurich, Zurich, Switzerland.
- Center for Microscopy and Image Analysis (ZMB), University of Zurich, Zurich, Switzerland.
| | - Fabian F Voigt
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Thomas Naert
- Institute of Anatomy and Zurich Kidney Center (ZKC), University of Zurich, Zurich, Switzerland
| | | | - Ruiyao Cai
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, Germany
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Anna Maria Reuss
- Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
- Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Shan Zhao
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Patricia Schmid
- Institute of Anatomy and Zurich Kidney Center (ZKC), University of Zurich, Zurich, Switzerland
| | - Sven Hildebrand
- Department of Cognitive Neuroscience, Faculty of Psychology & Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Martina Schaettin
- Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Dominik Groos
- Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - José María Mateos
- Center for Microscopy and Image Analysis (ZMB), University of Zurich, Zurich, Switzerland
| | - Philipp Bethge
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
| | - Taiyo Yamamoto
- Institute of Anatomy and Zurich Kidney Center (ZKC), University of Zurich, Zurich, Switzerland
| | - Valentino Aerne
- Department of Physics, University of Zurich, Zurich, Switzerland
| | - Alard Roebroeck
- Department of Cognitive Neuroscience, Faculty of Psychology & Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Ali Ertürk
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, Germany
| | - Adriano Aguzzi
- Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
- Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Urs Ziegler
- Center for Microscopy and Image Analysis (ZMB), University of Zurich, Zurich, Switzerland
| | - Esther Stoeckli
- University Research Priority Program (URPP), Adaptive Brain Circuits in Development and Learning, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Laura Baudis
- Department of Physics, University of Zurich, Zurich, Switzerland
| | - Soeren S Lienkamp
- Institute of Anatomy and Zurich Kidney Center (ZKC), University of Zurich, Zurich, Switzerland
| | - Fritjof Helmchen
- Brain Research Institute, University of Zurich, Zurich, Switzerland.
- University Research Priority Program (URPP), Adaptive Brain Circuits in Development and Learning, University of Zurich, Zurich, Switzerland.
- Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland.
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15
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Pozzi P, Balan V, Candeo A, Brix A, Pistocchi AS, D’Andrea C, Valentini G, Bassi A. Full-aperture extended-depth oblique plane microscopy through dynamic remote focusing. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:036502. [PMID: 38515831 PMCID: PMC10956707 DOI: 10.1117/1.jbo.29.3.036502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/02/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
Significance The reprojection setup typical of oblique plane microscopy (OPM) limits the effective aperture of the imaging system, and therefore its efficiency and resolution. Large aperture system is only possible through the use of custom specialized optics. A full-aperture OPM made with off the shelf components would both improve the performance of the method and encourage its widespread adoption. Aim To prove the feasibility of an OPM without a conventional reprojection setup, retaining the full aperture of the primary objective employed. Approach A deformable lens based remote focusing setup synchronized with the rolling shutter of a complementary metal-oxide semiconductor detector is used instead of a traditional reprojection system. Results The system was tested on microbeads, prepared slides, and zebrafish embryos. Resolution and pixel throughput were superior to conventional OPM with cropped apertures, and comparable with OPM implementations with custom made optical components. Conclusions An easily reproducible approach to OPM imaging is presented, eliminating the conventional reprojection setup and exploiting the full aperture of the employed objective.
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Affiliation(s)
- Paolo Pozzi
- Politecnico di Milano, Dipartimento di Fisica, Milano, Italy
| | - Vipin Balan
- Politecnico di Milano, Dipartimento di Fisica, Milano, Italy
| | - Alessia Candeo
- Politecnico di Milano, Dipartimento di Fisica, Milano, Italy
| | - Alessia Brix
- Università degli Studi di Milano, Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Milano, Italy
| | - Anna Silvia Pistocchi
- Università degli Studi di Milano, Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Milano, Italy
| | - Cosimo D’Andrea
- Politecnico di Milano, Dipartimento di Fisica, Milano, Italy
| | | | - Andrea Bassi
- Politecnico di Milano, Dipartimento di Fisica, Milano, Italy
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16
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Wang Y, Ye L. TESOS: an integrated approach for uniform mesoscale imaging. Cell Res 2024; 34:93-94. [PMID: 38168641 PMCID: PMC10837420 DOI: 10.1038/s41422-023-00888-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024] Open
Affiliation(s)
- Yu Wang
- Department of Neuroscience and Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Li Ye
- Department of Neuroscience and Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA.
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17
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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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18
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Carrette L, Santos A, Brennan M, Othman D, Collazo A, George O. Antagonists of the stress and opioid systems restore the functional connectivity of the prefrontal cortex during alcohol withdrawal through divergent mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.30.560339. [PMID: 37873478 PMCID: PMC10592857 DOI: 10.1101/2023.09.30.560339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Chronic alcohol consumption leads to dependence and withdrawal symptoms upon cessation, contributing to persistent use. However, the brain network mechanisms by which the brain orchestrates alcohol withdrawal and how these networks are affected by pharmacological treatments remain elusive. Recent work revealed that alcohol withdrawal produces a widespread increase in coordinated brain activity and a decrease in modularity of the whole-brain functional network using single-cell whole-brain imaging of immediate early genes. This decreased modularity and functional hyperconnectivity are hypothesized to be novel biomarkers of alcohol withdrawal in alcohol dependence, which could potentially be used to evaluate the efficacy of new medications for alcohol use disorder. However, there is no evidence that current FDA-approved medications or experimental treatments known to reduce alcohol drinking in animal models can normalize the changes in whole-brain functional connectivity. In this report, we tested the effect of R121919, a CRF1 antagonist, and naltrexone, an FDA-approved treatment for alcohol use disorder, on whole-brain functional connectivity using the cellular marker FOS combined with graph theory and advanced network analyses. Results show that both R121919 and naltrexone restored the functional connectivity of the prefrontal cortex during alcohol withdrawal, but through divergent mechanisms. Specifically, R121919 increased FOS activation in the prefrontal cortex, partially restored modularity, and normalized connectivity, particularly in CRF1-rich regions, including the prefrontal, pallidum, and extended amygdala circuits. On the other hand, naltrexone decreased FOS activation throughout the brain, decreased modularity, and increased connectivity overall except for the Mu opioid receptor-rich regions, including the thalamus. These results identify the brain networks underlying the pharmacological effects of R121919 and naltrexone and demonstrate that these drugs restored different aspects of functional connectivity of the prefrontal cortex, pallidum, amygdala, and thalamus during alcohol withdrawal. Notably, these effects were particularly prominent in CRF1- and Mu opioid receptors-rich regions highlighting the potential of whole-brain functional connectivity using FOS as a tool for identifying neuronal network mechanisms underlying the pharmacological effects of existing and new medications for alcohol use disorder.
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Affiliation(s)
- L.L.G. Carrette
- Department of Psychiatry, UC San Diego, La Jolla, CA, United States
| | - A. Santos
- Department of Psychiatry, UC San Diego, La Jolla, CA, United States
| | - M. Brennan
- Department of Psychiatry, UC San Diego, La Jolla, CA, United States
| | - D. Othman
- Department of Psychiatry, UC San Diego, La Jolla, CA, United States
| | - A. Collazo
- Beckman Institute, CalTech, Passadena, CA, United States
| | - O. George
- Department of Psychiatry, UC San Diego, La Jolla, CA, United States
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19
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Chen L, Meng J, Zhou Y, Zhao F, Ma Y, Feng W, Chen X, jin J, Gao S, Liu J, Zhang M, Liu A, Hong Z, Tang J, Kuang D, Huang L, Zhang Y, Fei P. Efficient 3D imaging and pathological analysis of the human lymphoma tumor microenvironment using light-sheet immunofluorescence microscopy. Theranostics 2024; 14:406-419. [PMID: 38164148 PMCID: PMC10750216 DOI: 10.7150/thno.86221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/26/2023] [Indexed: 01/03/2024] Open
Abstract
Rationale: The composition and spatial structure of the lymphoma tumor microenvironment (TME) provide key pathological insights for tumor survival and growth, invasion and metastasis, and resistance to immunotherapy. However, the 3D lymphoma TME has not been well studied owing to the limitations of current imaging techniques. In this work, we take full advantage of a series of new techniques to enable the first 3D TME study in intact lymphoma tissue. Methods: Diverse cell subtypes in lymphoma tissues were tagged using a multiplex immunofluorescence labeling technique. To optically clarify the entire tissue, immunolabeling-enabled three-dimensional imaging of solvent-cleared organs (iDISCO+), clear, unobstructed brain imaging cocktails and computational analysis (CUBIC) and stabilization to harsh conditions via intramolecular epoxide linkages to prevent degradation (SHIELD) were comprehensively compared with the ultimate dimensional imaging of solvent-cleared organs (uDISCO) approach selected for clearing lymphoma tissues. A Bessel-beam light-sheet fluorescence microscope (B-LSFM) was developed to three-dimensionally image the clarified tissues at high speed and high resolution. A customized MATLAB program was used to quantify the number and colocalization of the cell subtypes based on the acquired multichannel 3D images. By combining these cutting-edge methods, we successfully carried out high-efficiency 3D visualization and high-content cellular analyses of the lymphoma TME. Results: Several antibodies, including CD3, CD8, CD20, CD68, CD163, CD14, CD15, FOXP3 and Ki67, were screened for labeling the TME in lymphoma tumors. The 3D imaging results of the TME from three types of lymphoma, reactive lymphocytic hyperplasia (RLN), diffuse large B-cell lymphoma (DLBCL), and angioimmunoblastic T-cell lymphoma (AITL), were quantitatively analyzed, and their cell number, localization, and spatial correlation were comprehensively revealed. Conclusion: We present an advanced imaging-based method for efficient 3D visualization and high-content cellular analysis of the lymphoma TME, rendering it a valuable tool for tumor pathological diagnosis and other clinical research.
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Affiliation(s)
- Liting Chen
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiao Meng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hematology Department, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Yao Zhou
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Zhao
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Yifan Ma
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Wenyang Feng
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Xingyu Chen
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Jin jin
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shimeng Gao
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Jianchao Liu
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Man Zhang
- Hematology Department, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Aichun Liu
- Hematology Department, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Zhenya Hong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Tang
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Dong Kuang
- Department of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yicheng Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Fei
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
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20
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Murakami E, Nakamori M, Nakatani K, Shibata T, Tainaka K. Intracerebral Distribution of CAG Repeat-Binding Small Molecule Visualized by Whole-Brain Imaging. Bioconjug Chem 2023; 34:2187-2193. [PMID: 37948852 DOI: 10.1021/acs.bioconjchem.3c00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Understanding the pharmacokinetics of drug candidates of interest in the brain and evaluating drug delivery to the brain are important for developing drugs targeting the brain. Previously, we demonstrated that a CAG repeat-binding small molecule, naphthyridine-azaquinolone (NA), resulted in repeat contraction in mouse models of dentatorubral-pallidoluysian atrophy and Huntington's disease caused by aberrant expansion of CAG repeats. However, the intracerebral distribution and drug deliverability of NA remain unclear. Here, we report three-dimensional whole-brain imaging of an externally administered small molecule using tissue clearing and light sheet fluorescence microscopy (LSFM). We designed and synthesized an Alexa594-labeled NA derivative with a primary amine for whole-brain imaging (NA-Alexa594-NH2), revealing the intracerebral distribution of NA-Alexa594-NH2 after intraparenchymal and intracerebroventricular administrations by whole-brain imaging combined with tissue clearing and LSFM. We also clarified that intranasally administered NA-Alexa594-NH2 was delivered into the brain via multiple nose-to-brain pathways by tracking the time-dependent change in the intracerebral distribution. Whole-brain imaging of small molecules by tissue clearing and LSFM is useful for elucidating not only the intracerebral distribution but also the drug delivery pathways into the brain.
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Affiliation(s)
- Eitaro Murakami
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka 567-0047, Japan
| | - Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka 567-0047, Japan
| | - Tomonori Shibata
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka 567-0047, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Center for Bioresources, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
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21
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Vladimirov N, Voigt FF, Naert T, Araujo GR, Cai R, Reuss AM, Zhao S, Schmid P, Hildebrand S, Schaettin M, Groos D, Mateos JM, Bethge P, Yamamoto T, Aerne V, Roebroeck A, Ertürk A, Aguzzi A, Ziegler U, Stoeckli E, Baudis L, Lienkamp SS, Helmchen F. The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545256. [PMID: 38168219 PMCID: PMC10760166 DOI: 10.1101/2023.06.16.545256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In 2015, we launched the mesoSPIM initiative (www.mesospim.org), an open-source project for making light-sheet microscopy of large cleared tissues more accessible. Meanwhile, the demand for imaging larger samples at higher speed and resolution has increased, requiring major improvements in the capabilities of light-sheet microscopy. Here, we introduce the next-generation mesoSPIM ("Benchtop") with significantly increased field of view, improved resolution, higher throughput, more affordable cost and simpler assembly compared to the original version. We developed a new method for testing objectives, enabling us to select detection objectives optimal for light-sheet imaging with large-sensor sCMOS cameras. The new mesoSPIM achieves high spatial resolution (1.5 μm laterally, 3.3 μm axially) across the entire field of view, a magnification up to 20x, and supports sample sizes ranging from sub-mm up to several centimetres, while being compatible with multiple clearing techniques. The new microscope serves a broad range of applications in neuroscience, developmental biology, and even physics.
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Affiliation(s)
- Nikita Vladimirov
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- University Research Priority Program (URPP) Adaptive Brain Circuits in Development and Learning (AdaBD), University of Zurich, Zurich, Switzerland
- Center for Microscopy and Image Analysis (ZMB), University of Zurich, Zurich, Switzerland
| | - Fabian F. Voigt
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
- Present address: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Thomas Naert
- Institute of Anatomy and Zurich Kidney Center (ZKC), University of Zurich, Zurich, Switzerland
| | | | - Ruiyao Cai
- Present address: Department of Biology, Stanford University, Stanford, CA, USA
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, German
| | - Anna Maria Reuss
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
- Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Shan Zhao
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Patricia Schmid
- Institute of Anatomy and Zurich Kidney Center (ZKC), University of Zurich, Zurich, Switzerland
| | - Sven Hildebrand
- Department of Cognitive Neuroscience, Faculty of Psychology & Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Martina Schaettin
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Dominik Groos
- Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - José María Mateos
- Center for Microscopy and Image Analysis (ZMB), University of Zurich, Zurich, Switzerland
| | - Philipp Bethge
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
| | - Taiyo Yamamoto
- Institute of Anatomy and Zurich Kidney Center (ZKC), University of Zurich, Zurich, Switzerland
| | - Valentino Aerne
- Department of Physics, University of Zurich, Zurich, Switzerland
| | - Alard Roebroeck
- Department of Cognitive Neuroscience, Faculty of Psychology & Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Ali Ertürk
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, Munich, German
| | - Adriano Aguzzi
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
- Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Urs Ziegler
- Center for Microscopy and Image Analysis (ZMB), University of Zurich, Zurich, Switzerland
| | - Esther Stoeckli
- University Research Priority Program (URPP) Adaptive Brain Circuits in Development and Learning (AdaBD), University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Laura Baudis
- Department of Physics, University of Zurich, Zurich, Switzerland
| | - Soeren S. Lienkamp
- Institute of Anatomy and Zurich Kidney Center (ZKC), University of Zurich, Zurich, Switzerland
| | - Fritjof Helmchen
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- University Research Priority Program (URPP) Adaptive Brain Circuits in Development and Learning (AdaBD), University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
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22
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Doyle MA, Taylor A, Winder DG. Neural Circuitries and Alcohol Use Disorder: Cutting Corners in the Cycle. Curr Top Behav Neurosci 2023. [PMID: 38082108 DOI: 10.1007/7854_2023_454] [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] [Indexed: 02/19/2024]
Abstract
An implicit tenet of the alcohol use disorder (AUD) research field is that knowledge of how alcohol interacts with the brain is critical to the development of an understanding of vulnerability to AUD and treatment approaches. Gaining this understanding requires the mapping of brain function critical to specific components of this heterogeneous disorder. Early approaches in humans and animal models focused on the determination of specific brain regions sensitive to alcohol action and their participation in AUD-relevant behaviors. Broadly speaking, this research has focused on three domains, Binge/Intoxication, Negative Affect/Withdrawal, and Preoccupation/Anticipation, with a number of regions identified as participating in each. With the generational advances in technologies that the field of neuroscience has undergone over the last two decades, this focus has shifted to a circuit-based analysis. A wealth of new data has sharpened the field's focus on the specific roles of the interconnectivity of multiple brain regions in AUD and AUD-relevant behaviors, as well as demonstrating that the three major domains described above have much fuzzier edges than originally thought.In this chapter, we very briefly review brain regions previously implicated in aspects of AUD-relevant behavior from animal model research. Next, we move to a more in-depth overview of circuit-based approaches, and the utilization of these approaches in current AUD research.
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Affiliation(s)
- Marie A Doyle
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Center for Addiction Research, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Anne Taylor
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Center for Addiction Research, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Danny G Winder
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt Center for Addiction Research, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.
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23
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Jiang T, Gong H, Yuan J. Whole-brain Optical Imaging: A Powerful Tool for Precise Brain Mapping at the Mesoscopic Level. Neurosci Bull 2023; 39:1840-1858. [PMID: 37715920 PMCID: PMC10661546 DOI: 10.1007/s12264-023-01112-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/08/2023] [Indexed: 09/18/2023] Open
Abstract
The mammalian brain is a highly complex network that consists of millions to billions of densely-interconnected neurons. Precise dissection of neural circuits at the mesoscopic level can provide important structural information for understanding the brain. Optical approaches can achieve submicron lateral resolution and achieve "optical sectioning" by a variety of means, which has the natural advantage of allowing the observation of neural circuits at the mesoscopic level. Automated whole-brain optical imaging methods based on tissue clearing or histological sectioning surpass the limitation of optical imaging depth in biological tissues and can provide delicate structural information in a large volume of tissues. Combined with various fluorescent labeling techniques, whole-brain optical imaging methods have shown great potential in the brain-wide quantitative profiling of cells, circuits, and blood vessels. In this review, we summarize the principles and implementations of various whole-brain optical imaging methods and provide some concepts regarding their future development.
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Affiliation(s)
- Tao Jiang
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
| | - Hui Gong
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jing Yuan
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
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24
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Ryu Y, Kim Y, Park SJ, Kim SR, Kim HJ, Ha CM. Comparison of Light-Sheet Fluorescence Microscopy and Fast-Confocal Microscopy for Three-Dimensional Imaging of Cleared Mouse Brain. Methods Protoc 2023; 6:108. [PMID: 37987355 PMCID: PMC10660704 DOI: 10.3390/mps6060108] [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: 08/18/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023] Open
Abstract
Whole-brain imaging is important for understanding brain functions through deciphering tissue structures, neuronal circuits, and single-neuron tracing. Thus, many clearing methods have been developed to acquire whole-brain images or images of three-dimensional thick tissues. However, there are several limitations to imaging whole-brain volumes, including long image acquisition times, large volumes of data, and a long post-image process. Based on these limitations, many researchers are unsure about which light microscopy is most suitable for imaging thick tissues. Here, we compared fast-confocal microscopy with light-sheet fluorescence microscopy for whole-brain three-dimensional imaging, which can acquire images the fastest. To compare the two types of microscopies for large-volume imaging, we performed tissue clearing of a whole mouse brain, and changed the sample chamber and low- magnification objective lens and modified the sample holder of a light-sheet fluorescence microscope. We found out that light-sheet fluorescence microscopy using a 2.5× objective lens possesses several advantages, including saving time, large-volume image acquisitions, and high Z-resolution, over fast-confocal microscopy, which uses a 4× objective lens. Therefore, we suggest that light-sheet fluorescence microscopy is suitable for whole mouse brain imaging and for obtaining high-resolution three-dimensional images.
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Affiliation(s)
- Youngjae Ryu
- Research Strategy Office and Brain Research Core Facilities of Korea Brain Research Institute, Daegu 41062, Republic of Korea; (Y.R.); (Y.K.)
- Department of Histology, College of Veterinary Medicine, Kyungpook University, Daegu 41566, Republic of Korea;
| | - Yoonju Kim
- Research Strategy Office and Brain Research Core Facilities of Korea Brain Research Institute, Daegu 41062, Republic of Korea; (Y.R.); (Y.K.)
| | - Sang-Joon Park
- Department of Histology, College of Veterinary Medicine, Kyungpook University, Daegu 41566, Republic of Korea;
| | - Sung Rae Kim
- Dementia Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea; (S.R.K.); (H.-J.K.)
| | - Hyung-Jun Kim
- Dementia Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea; (S.R.K.); (H.-J.K.)
| | - Chang Man Ha
- Research Strategy Office and Brain Research Core Facilities of Korea Brain Research Institute, Daegu 41062, Republic of Korea; (Y.R.); (Y.K.)
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25
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Park S, Na M, Chang S, Kim KH. High-resolution open-top axially swept light sheet microscopy. BMC Biol 2023; 21:248. [PMID: 37940973 PMCID: PMC10634022 DOI: 10.1186/s12915-023-01747-3] [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: 04/19/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Open-top light-sheet microscopy (OT-LSM) is a specialized microscopic technique for the high-throughput cellular imaging of optically cleared, large-sized specimens, such as the brain. Despite the development of various OT-LSM techniques, achieving submicron resolution in all dimensions remains. RESULTS We developed a high-resolution open-top axially swept LSM (HR-OTAS-LSM) for high-throughput and high-resolution imaging in all dimensions. High axial and lateral resolutions were achieved by using an aberration-corrected axially swept excitation light sheet in the illumination arm and a high numerical aperture (NA) immersion objective lens in the imaging arm, respectively. The high-resolution, high-throughput visualization of neuronal networks in mouse brain and retina specimens validated the performance of HR-OTAS-LSM. CONCLUSIONS The proposed HR-OTAS-LSM method represents a significant advancement in the high-resolution mapping of cellular networks in biological systems such as the brain and retina.
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Affiliation(s)
- Soohyun Park
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Myeongsu Na
- Department of Research and Development Center, Crayon Technologies, 19 Sanmaru-ro, Guri, Gyeonggi-do, 11901, Republic of Korea
| | - Sunghoe Chang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Ki Hean Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
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26
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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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27
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Balaram P, Takasaki K, Hellevik A, Tandukar J, Turschak E, MacLennan B, Ouellette N, Torres R, Laughland C, Gliko O, Seshamani S, Perlman E, Taormina M, Peterson E, Juneau Z, Potekhina L, Glaser A, Chandrashekar J, Logsdon M, Cao K, Dylla C, Hatanaka G, Chatterjee S, Ting J, Vumbaco D, Waters J, Bair W, Tsao D, Gao R, Reid C. Microscale visualization of cellular features in adult macaque visual cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.02.565381. [PMID: 37961179 PMCID: PMC10635096 DOI: 10.1101/2023.11.02.565381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Expansion microscopy and light sheet imaging enable fine-scale resolution of intracellular features that comprise neural circuits. Most current techniques visualize sparsely distributed features across whole brains or densely distributed features within individual brain regions. Here, we visualize dense distributions of immunolabeled proteins across early visual cortical areas in adult macaque monkeys. This process may be combined with multiphoton or magnetic resonance imaging to produce multimodal atlases in large, gyrencephalic brains.
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Ma C, Xia D, Huang S, Du Q, Liu J, Zhang B, Zhu Q, Bi G, Wang H, Xu RX. High precision vibration sectioning for 3D imaging of the whole central nervous system. J Neurosci Methods 2023; 399:109966. [PMID: 37666283 DOI: 10.1016/j.jneumeth.2023.109966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/21/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Imaging and reconstruction of the morphology of neurons within the entire central nervous system (CNS) is important for deciphering the neural circuitry and related brain functions. With combination of tissue clearing and light sheet microscopy, previous studies have imaged the mouse CNS at cellular resolution, while remaining single axons unresolvable due to the tradeoff between sample size and imaging resolution. This could be improved by sectioning the sample into thick slices and imaged with high resolution light sheet microscopy as described in our previous study. However, the achievable quality for 3D imaging of serial thick slices is often hindered by surface undulation and other artifacts introduced by sectioning and handling limitations. NEW METHODS In order to improve the imaging quality for mouse CNS, we develop a high-performance vibratome system for sample sectioning and handling automation. The sectioning mechanism of the system was modeled theoretically and verified experimentally. The effects of process parameters and sample properties on sectioning accuracy were studied to optimize the sectioning outcome. The resultant imaging outcome was demonstrated on mouse samples. RESULTS Our theoretical model of vibratome effectively depicts the relationship between the sample surface undulation errors and the sectioning parameters. With the guidance of the theoretical model, the vibratome is able to achieve a local surface undulation error of ±0.5 µm and a surface arithmetic mean deviation (Sa) of 220 nm for 300-μm-thick tissue slices. Imaging results of mouse CNS show the continuous sectioning capability of the vibratome. COMPARISON WITH EXISTING METHOD Our automatic sectioning and handling system is able to process serial thick slices for 3D imaging of the whole CNS at a single-axon resolution, superior to the commercially available vibratome devices. CONCLUSION Our automatic sectioning and handling system can be optimized to prepare thick sample slices with minimal surface undulation and manual manipulation in support of 3D brain mapping with high-throughput and high-accuracy.
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Affiliation(s)
- Canzhen Ma
- School of Engineering Science, University of Science and Technology of China, Hefei 230027, China; Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; School of Biomedical Engineering, University of Science and Technology of China, Suzhou 215123, China
| | - Debin Xia
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, University of Science and Technology of China, Hefei 230027, China
| | - Shichang Huang
- Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Qing Du
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
| | - Jiajun Liu
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, University of Science and Technology of China, Hefei 230027, China
| | - Bo Zhang
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, University of Science and Technology of China, Hefei 230027, China
| | - Qingyuan Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Guoqiang Bi
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Hao Wang
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, University of Science and Technology of China, Hefei 230027, China.
| | - Ronald X Xu
- School of Engineering Science, University of Science and Technology of China, Hefei 230027, China; School of Biomedical Engineering, University of Science and Technology of China, Suzhou 215123, China.
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29
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Costantini I, Morgan L, Yang J, Balbastre Y, Varadarajan D, Pesce L, Scardigli M, Mazzamuto G, Gavryusev V, Castelli FM, Roffilli M, Silvestri L, Laffey J, Raia S, Varghese M, Wicinski B, Chang S, Chen IA, Wang H, Cordero D, Vera M, Nolan J, Nestor K, Mora J, Iglesias JE, Garcia Pallares E, Evancic K, Augustinack JC, Fogarty M, Dalca AV, Frosch MP, Magnain C, Frost R, van der Kouwe A, Chen SC, Boas DA, Pavone FS, Fischl B, Hof PR. A cellular resolution atlas of Broca's area. SCIENCE ADVANCES 2023; 9:eadg3844. [PMID: 37824623 PMCID: PMC10569704 DOI: 10.1126/sciadv.adg3844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/03/2023] [Indexed: 10/14/2023]
Abstract
Brain cells are arranged in laminar, nuclear, or columnar structures, spanning a range of scales. Here, we construct a reliable cell census in the frontal lobe of human cerebral cortex at micrometer resolution in a magnetic resonance imaging (MRI)-referenced system using innovative imaging and analysis methodologies. MRI establishes a macroscopic reference coordinate system of laminar and cytoarchitectural boundaries. Cell counting is obtained with a digital stereological approach on the 3D reconstruction at cellular resolution from a custom-made inverted confocal light-sheet fluorescence microscope (LSFM). Mesoscale optical coherence tomography enables the registration of the distorted histological cell typing obtained with LSFM to the MRI-based atlas coordinate system. The outcome is an integrated high-resolution cellular census of Broca's area in a human postmortem specimen, within a whole-brain reference space atlas.
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Affiliation(s)
- Irene Costantini
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- Department of Biology, University of Florence, Florence, Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Leah Morgan
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - Jiarui Yang
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Yael Balbastre
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Divya Varadarajan
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Luca Pesce
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
| | - Marina Scardigli
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino (FI), Italy
- Division of Physiology, Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Giacomo Mazzamuto
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino (FI), Italy
| | - Vladislav Gavryusev
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino (FI), Italy
| | - Filippo Maria Castelli
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino (FI), Italy
- Bioretics srl, Cesena, Italy
| | | | - Ludovico Silvestri
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino (FI), Italy
| | - Jessie Laffey
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sophia Raia
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Merina Varghese
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bridget Wicinski
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shuaibin Chang
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | | | - Hui Wang
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Devani Cordero
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - Matthew Vera
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - Jackson Nolan
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - Kimberly Nestor
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Jocelyn Mora
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Juan Eugenio Iglesias
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Erendira Garcia Pallares
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - Kathryn Evancic
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Jean C. Augustinack
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Morgan Fogarty
- Imaging Science Program, Washington University McKelvey School of Engineering, St. Louis, MO, USA
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Adrian V. Dalca
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew P. Frosch
- C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Caroline Magnain
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Robert Frost
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Andre van der Kouwe
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | - Shih-Chi Chen
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - David A. Boas
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Francesco Saverio Pavone
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino (FI), Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino (FI), Italy
| | - Bruce Fischl
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- HST, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Patrick R. Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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30
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Ziak J, Dorskind J, Trigg B, Sudarsanam S, Hand R, Kolodkin AL. MAP1B Regulates Cortical Neuron Interstitial Axon Branching Through the Tubulin Tyrosination Cycle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560024. [PMID: 37873083 PMCID: PMC10592918 DOI: 10.1101/2023.10.02.560024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Regulation of directed axon guidance and branching during development is essential for the generation of neuronal networks. However, the molecular mechanisms that underlie interstitial axon branching in the mammalian brain remain unresolved. Here, we investigate interstitial axon branching in vivo using an approach for precise labeling of layer 2/3 callosal projection neurons (CPNs), allowing for quantitative analysis of axonal morphology at high acuity and also manipulation of gene expression in well-defined temporal windows. We find that the GSK3β serine/threonine kinase promotes interstitial axon branching in layer 2/3 CPNs by releasing MAP1B-mediated inhibition of axon branching. Further, we find that the tubulin tyrosination cycle is a key downstream component of GSK3β/MAP1B signaling. We propose that MAP1B functions as a brake on axon branching that can be released by GSK3β activation, regulating the tubulin code and thereby playing an integral role in sculpting cortical neuron axon morphology.
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Affiliation(s)
- Jakub Ziak
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD 21205
| | - Joelle Dorskind
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD 21205
- Novartis Institutes for BioMedical Research, Boston, MA
| | - Brian Trigg
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD 21205
| | - Sriram Sudarsanam
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD 21205
| | - Randal Hand
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD 21205
- Prilenia Therapeutics, Boston, MA
| | - Alex L. Kolodkin
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins Kavli Neuroscience Discovery Institute, The Johns Hopkins School of Medicine, 725 North Wolfe St., Baltimore, MD 21205
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31
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Bjerke IE, Yates SC, Carey H, Bjaalie JG, Leergaard TB. Scaling up cell-counting efforts in neuroscience through semi-automated methods. iScience 2023; 26:107562. [PMID: 37636060 PMCID: PMC10457595 DOI: 10.1016/j.isci.2023.107562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
Quantifying how the cellular composition of brain regions vary across development, aging, sex, and disease, is crucial in experimental neuroscience, and the accuracy of different counting methods is continuously debated. Due to the tedious nature of most counting procedures, studies are often restricted to one or a few brain regions. Recently, there have been considerable methodological advances in combining semi-automated feature extraction with brain atlases for cell quantification. Such methods hold great promise for scaling up cell-counting efforts. However, little focus has been paid to how these methods should be implemented and reported to support reproducibility. Here, we provide an overview of practices for conducting and reporting cell counting in mouse and rat brains, showing that critical details for interpretation are typically lacking. We go on to discuss how novel methods may increase efficiency and reproducibility of cell counting studies. Lastly, we provide practical recommendations for researchers planning cell counting.
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Affiliation(s)
- Ingvild Elise Bjerke
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Sharon Christine Yates
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Harry Carey
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan Gunnar Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve Brauns Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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32
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Schregel K, Heinz L, Hunger J, Pan C, Bode J, Fischer M, Sturm V, Venkataramani V, Karimian-Jazi K, Agardy DA, Streibel Y, Zerelles R, Wick W, Heiland S, Bunse T, Tews B, Platten M, Winkler F, Bendszus M, Breckwoldt MO. A Cellular Ground Truth to Develop MRI Signatures in Glioma Models by Correlative Light Sheet Microscopy and Atlas-Based Coregistration. J Neurosci 2023; 43:5574-5587. [PMID: 37429718 PMCID: PMC10376935 DOI: 10.1523/jneurosci.1470-22.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 05/21/2023] [Accepted: 06/25/2023] [Indexed: 07/12/2023] Open
Abstract
Glioblastoma is the most common malignant primary brain tumor with poor overall survival. Magnetic resonance imaging (MRI) is the main imaging modality for glioblastoma but has inherent shortcomings. The molecular and cellular basis of MR signals is incompletely understood. We established a ground truth-based image analysis platform to coregister MRI and light sheet microscopy (LSM) data to each other and to an anatomic reference atlas for quantification of 20 predefined anatomic subregions. Our pipeline also includes a segmentation and quantification approach for single myeloid cells in entire LSM datasets. This method was applied to three preclinical glioma models in male and female mice (GL261, U87MG, and S24), which exhibit different key features of the human glioma. Multiparametric MR data including T2-weighted sequences, diffusion tensor imaging, T2 and T2* relaxometry were acquired. Following tissue clearing, LSM focused on the analysis of tumor cell density, microvasculature, and innate immune cell infiltration. Correlated analysis revealed differences in quantitative MRI metrics between the tumor-bearing and the contralateral hemisphere. LSM identified tumor subregions that differed in their MRI characteristics, indicating tumor heterogeneity. Interestingly, MRI signatures, defined as unique combinations of different MRI parameters, differed greatly between the models. The direct correlation of MRI and LSM allows an in-depth characterization of preclinical glioma and can be used to decipher the structural, cellular, and, likely, molecular basis of tumoral MRI biomarkers. Our approach may be applied in other preclinical brain tumor or neurologic disease models, and the derived MRI signatures could ultimately inform image interpretation in a clinical setting.SIGNIFICANCE STATEMENT We established a histologic ground truth-based approach for MR image analyses and tested this method in three preclinical glioma models exhibiting different features of glioblastoma. Coregistration of light sheet microscopy to MRI allowed for an evaluation of quantitative MRI data in histologically distinct tumor subregions. Coregistration to a mouse brain atlas enabled a regional comparison of MRI parameters with a histologically informed interpretation of the results. Our approach is transferable to other preclinical models of brain tumors and further neurologic disorders. The method can be used to decipher the structural, cellular, and molecular basis of MRI signal characteristics. Ultimately, information derived from such analyses could strengthen the neuroradiological evaluation of glioblastoma as they enhance the interpretation of MRI data.
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Affiliation(s)
- Katharina Schregel
- Department of Neuroradiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lennart Heinz
- Department of Neuroradiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Jessica Hunger
- Department of Neuroradiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Chenchen Pan
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Neurology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Julia Bode
- Molecular Mechanisms of Tumor Invasion, Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Manuel Fischer
- Department of Neuroradiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Volker Sturm
- Department of Neuroradiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Varun Venkataramani
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Neurology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Kianush Karimian-Jazi
- Department of Neuroradiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Dennis A Agardy
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, 68167 Mannheim, Germany
| | - Yannik Streibel
- Department of Neuroradiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Roland Zerelles
- Department of Neuroradiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Neurology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Sabine Heiland
- Department of Neuroradiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Theresa Bunse
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, 68167 Mannheim, Germany
| | - Björn Tews
- Molecular Mechanisms of Tumor Invasion, Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences, Heidelberg University, 68167 Mannheim, Germany
| | - Frank Winkler
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Neurology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Michael O Breckwoldt
- Department of Neuroradiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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33
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Skovbjerg G, Roostalu U, Salinas CG, Skytte JL, Perens J, Clemmensen C, Elster L, Frich CK, Hansen HH, Hecksher-Sørensen J. Uncovering CNS access of lipidated exendin-4 analogues by quantitative whole-brain 3D light sheet imaging. Neuropharmacology 2023:109637. [PMID: 37391028 DOI: 10.1016/j.neuropharm.2023.109637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 07/02/2023]
Abstract
Peptide-based drug development for CNS disorders is challenged by poor blood-brain barrier (BBB) penetrability of peptides. While acylation protractions (lipidation) have been successfully applied to increase circulating half-life of therapeutic peptides, little is known about the CNS accessibility of lipidated peptide drugs. Light-sheet fluorescence microscopy (LSFM) has emerged as a powerful method to visualize whole-brain 3D distribution of fluorescently labelled therapeutic peptides at single-cell resolution. Here, we applied LSFM to map CNS distribution of the clinically relevant GLP-1 receptor agonist (GLP-1RA) exendin-4 (Ex4) and lipidated analogues following peripheral administration. Mice received an intravenous dose (100 nmol/kg) of IR800 fluorophore-labelled Ex4 (Ex4), Ex4 acylated with a C16-monoacid (Ex4_C16MA) or C18-diacid (Ex4_C18DA). Other mice were administered C16MA-acylated exendin 9-39 (Ex9-39_C16MA), a selective GLP-1R antagonist, serving as negative control for GLP-1R mediated agonist internalization. Two hours post-dosing, brain distribution of Ex4 and analogues was predominantly restricted to the circumventricular organs, notably area postrema and nucleus of the solitary tract. Ex4_C16MA and Ex9-39_C16MA also distributed to the paraventricular hypothalamic nucleus and medial habenula. Notably, Ex4_C18DA was detected in deeper-lying brain structures such as dorsomedial/ventromedial hypothalamic nuclei and the dentate gyrus. Similar CNS distribution maps of Ex4-C16MA and Ex9-39_C16MA suggest that brain access of lipidated Ex4 analogues is independent on GLP-1 receptor internalization. The cerebrovasculature was devoid of specific labelling, hence not supporting a direct role of GLP-1 RAs in BBB function. In conclusion, peptide lipidation increases CNS accessibility of Ex4. Our fully automated LSFM pipeline is suitable for mapping whole-brain distribution of fluorescently labelled drugs.
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Affiliation(s)
- Grethe Skovbjerg
- Gubra ApS, Hørsholm Kongevej 11B, 2970, Hørsholm, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Urmas Roostalu
- Gubra ApS, Hørsholm Kongevej 11B, 2970, Hørsholm, Denmark
| | | | - Jacob L Skytte
- Gubra ApS, Hørsholm Kongevej 11B, 2970, Hørsholm, Denmark
| | - Johanna Perens
- Gubra ApS, Hørsholm Kongevej 11B, 2970, Hørsholm, Denmark
| | - Christoffer Clemmensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Lisbeth Elster
- Gubra ApS, Hørsholm Kongevej 11B, 2970, Hørsholm, Denmark
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Qi X, Muñoz-Castañeda R, Narasimhan A, Ding L, Chen X, Elowsky C, Palmer J, Drewes R, Sun J, Mizrachi J, Peng H, Wu Z, Osten P. High-throughput confocal airy beam oblique light-sheet tomography of brain-wide imaging at single-cell resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.04.543586. [PMID: 37333143 PMCID: PMC10274617 DOI: 10.1101/2023.06.04.543586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Brain research is an area of research characterized by its cutting-edge nature, with brain mapping constituting a crucial aspect of this field. As sequencing tools have played a crucial role in gene sequencing, brain mapping largely depends on automated, high-throughput and high-resolution imaging techniques. Over the years, the demand for high-throughput imaging has scaled exponentially with the rapid development of microscopic brain mapping. In this paper, we introduce the novel concept of confocal Airy beam into oblique light-sheet tomography named CAB-OLST. We demonstrate that this technique enables the high throughput of brain-wide imaging of long-distance axon projection for the entire mouse brain at a resolution of 0.26 μm × 0.26 μm × 1.06 μm in 58 hours. This technique represents an innovative contribution to the field of brain research by setting a new standard for high-throughput imaging techniques.
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Carrette LLG, Kimbrough A, Davoudian PA, Kwan AC, Collazo A, George O. Hyperconnectivity of Two Separate Long-Range Cholinergic Systems Contributes to the Reorganization of the Brain Functional Connectivity during Nicotine Withdrawal in Male Mice. eNeuro 2023; 10:ENEURO.0019-23.2023. [PMID: 37295945 PMCID: PMC10306126 DOI: 10.1523/eneuro.0019-23.2023] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 06/12/2023] Open
Abstract
Chronic nicotine results in dependence with withdrawal symptoms on discontinuation of use, through desensitization of nicotinic acetylcholine receptors and altered cholinergic neurotransmission. Nicotine withdrawal is associated with increased whole-brain functional connectivity and decreased network modularity; however, the role of cholinergic neurons in those changes is unknown. To identify the contribution of nicotinic receptors and cholinergic regions to changes in the functional network, we analyzed the contribution of the main cholinergic regions to brain-wide activation of the immediate early-gene Fos during withdrawal in male mice and correlated these changes with the expression of nicotinic receptor mRNA throughout the brain. We show that the main functional connectivity modules included the main long-range cholinergic regions, which were highly synchronized with the rest of the brain. However, despite this hyperconnectivity, they were organized into two anticorrelated networks that were separated into basal forebrain-projecting and brainstem-thalamic-projecting cholinergic regions, validating a long-standing hypothesis of the organization of the brain cholinergic systems. Moreover, baseline (without nicotine) expression of Chrna2, Chrna3, Chrna10, and Chrnd mRNA of each brain region correlated with withdrawal-induced changes in Fos expression. Finally, by mining the Allen Brain mRNA expression database, we were able to identify 1755 gene candidates and three pathways (Sox2-Oct4-Nanog, JAK-STAT, and MeCP2-GABA) that may contribute to nicotine withdrawal-induced Fos expression. These results identify the dual contribution of the basal forebrain and brainstem-thalamic cholinergic systems to whole-brain functional connectivity during withdrawal; and identify nicotinic receptors and novel cellular pathways that may be critical for the transition to nicotine dependence.
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Affiliation(s)
| | - Adam Kimbrough
- Department of Psychiatry, UC San Diego, California 92093
| | - Pasha A Davoudian
- Medical Scientist Training Program, Yale University School of Medicine, New Haven, Connecticut 06511
- Interdepartmental Neuroscience Program, Yale University School of Medicine, New Haven, Connecticut 06511
| | - Alex C Kwan
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853
| | - Andres Collazo
- Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Olivier George
- Department of Psychiatry, UC San Diego, California 92093
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Zhu T, Nie J, Yu T, Zhu D, Huang Y, Chen Z, Gu Z, Tang J, Li D, Fei P. Large-scale high-throughput 3D culture, imaging, and analysis of cell spheroids using microchip-enhanced light-sheet microscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:1659-1669. [PMID: 37078040 PMCID: PMC10110308 DOI: 10.1364/boe.485217] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/24/2023] [Accepted: 03/06/2023] [Indexed: 05/03/2023]
Abstract
Light sheet microscopy combined with a microchip is an emerging tool in biomedical research that notably improves efficiency. However, microchip-enhanced light-sheet microscopy is limited by noticeable aberrations induced by the complex refractive indices in the chip. Herein, we report a droplet microchip that is specifically engineered to be capable of large-scale culture of 3D spheroids (over 600 samples per chip) and has a polymer index matched to water (difference <1%). When combined with a lab-built open-top light-sheet microscope, this microchip-enhanced microscopy technique allows 3D time-lapse imaging of the cultivated spheroids with ∼2.5-µm single-cell resolution and a high throughput of ∼120 spheroids per minute. This technique was validated by a comparative study on the proliferation and apoptosis rates of hundreds of spheroids with or without treatment with the apoptosis-inducing drug Staurosporine.
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Affiliation(s)
- Tingting Zhu
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jun Nie
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Tingting Yu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yanyi Huang
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
- College of Chemistry, Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Zaozao Chen
- State Key Laboratory of Bioelectronics School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jiang Tang
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dongyu Li
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Peng Fei
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, China
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Ha BG, Jang YJ, Lee E, Kim BG, Myung K, Sun W, Jeong SJ. Isolation and identification of extracellular matrix proteins from oil-based CASPERized mouse brains for matrisomal analysis. Heliyon 2023; 9:e14777. [PMID: 37025807 PMCID: PMC10070542 DOI: 10.1016/j.heliyon.2023.e14777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 03/02/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
The extracellular matrix (ECM) components present within all tissues and organs help to maintain the cytoskeletal architecture and tissue morphology. Although the ECM plays a role in cellular events and signaling pathways, it has not been well studied due its insolubility and complexity. Brain tissue has a higher cell density and weaker mechanical strength than other tissues in the body. When removing cells using a general decellularization method to produce scaffolds and obtain ECM proteins, various problems must be considered because tissues are easily damaged. To retain the brain shape and ECM components, we performed decellularization in combination with polymerization. We immersed mouse brains in oil for polymerization and decellularization via O-CASPER (Oil-based Clinically and Experimentally Applicable Acellular Tissue Scaffold Production for Tissue Engineering and Regenerative Medicine) and then isolated ECM components using sequential matrisome preparation reagents (SMPRs), namely, RIPA, PNGase F, and concanavalin A. Adult mouse brains were preserved with our decellularization method. Western blot and LC-MS/MS analyses revealed that ECM components, including collagen and laminin, were isolated efficiently from decellularized mouse brains using SMPRs. Our method will be useful to obtain matrisomal data and perform functional studies using adult mouse brains and other tissues.
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Affiliation(s)
- Byung Geun Ha
- Research Group of Developmental Disorders and Rare Diseases, Korea Brain Research Institute (KBRI), Daegu, 41062, Republic of Korea
| | - Yu-Jin Jang
- Research Group of Developmental Disorders and Rare Diseases, Korea Brain Research Institute (KBRI), Daegu, 41062, Republic of Korea
| | - EunSoo Lee
- Fluorescence Core Imaging Center, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Woong Sun
- Department of Anatomy, Brain Korea 21 Plus Program for Biomedical Science, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Sung-Jin Jeong
- Research Group of Developmental Disorders and Rare Diseases, Korea Brain Research Institute (KBRI), Daegu, 41062, Republic of Korea
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea
- Corresponding author.Research Group of Developmental Disorders and Rare Diseases, Korea Brain Research Institute (KBRI), Daegu, 41062, Republic of Korea.
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Carrette LL, Kimbrough A, Davoudian PA, Kwan AC, Collazo A, George O. Hyperconnectivity of two separate long-range cholinergic systems contributes to the reorganization of the brain functional connectivity during nicotine withdrawal in male mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534836. [PMID: 37034602 PMCID: PMC10081261 DOI: 10.1101/2023.03.29.534836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Chronic nicotine results in dependence with withdrawal symptoms upon discontinuation of use, through desensitization of nicotinic acetylcholine receptors and altered cholinergic neurotransmission. Nicotine withdrawal is associated with increased whole-brain functional connectivity and decreased network modularity, however, the role of cholinergic neurons in those changes is unknown. To identify the contribution of nicotinic receptors and cholinergic regions to changes in the functional network, we analyzed the contribution of the main cholinergic regions to brain-wide activation of the immediate early-gene FOS during withdrawal in male mice and correlated these changes with the expression of nicotinic receptor mRNA throughout the brain. We show that the main functional connectivity modules included the main long-range cholinergic regions, which were highly synchronized with the rest of the brain. However, despite this hyperconnectivity they were organized into two anticorrelated networks that were separated into basal forebrain projecting and brainstem-thalamic projecting cholinergic regions, validating a long-standing hypothesis of the organization of the brain cholinergic systems. Moreover, baseline (without nicotine) expression of Chrna2 , Chrna3 , Chrna10 , and Chrnd mRNA of each brain region correlated with withdrawal-induced changes in FOS expression. Finally, by mining the Allen Brain mRNA expression database, we were able to identify 1755 gene candidates and three pathways (Sox2-Oct4-Nanog, JAK-STAT, and MeCP2-GABA) that may contribute to nicotine withdrawal-induced FOS expression. These results identify the dual contribution of the basal forebrain and brainstem-thalamic cholinergic systems to whole-brain functional connectivity during withdrawal; and identify nicotinic receptors and novel cellular pathways that may be critical for the transition to nicotine dependence. Significance Statement Discontinuation of nicotine use in dependent users is associated with increased whole-brain activation and functional connectivity and leads to withdrawal symptoms. Here we investigated the contribution of the nicotinic cholinergic receptors and main cholinergic projecting brain areas in the whole-brain changes associated with withdrawal. This not only allowed us to visualize and confirm the previously described duality of the cholinergic brain system using this novel methodology, but also identify nicotinic receptors together with 1751 other genes that contribute, and could thus be targets for treatments against, nicotine withdrawal and dependence.
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Affiliation(s)
| | - Adam Kimbrough
- Department of Psychiatry, UC San Diego, La Jolla, CA, 92032, United States
| | - Pasha A. Davoudian
- Medical Scientist Training Program, Yale University School of Medicine, New Haven, CT, 06511, United States
- Interdepartmental Neuroscience Program, Yale University School of Medicine, New Haven, CT, 06511, United States
| | - Alex C. Kwan
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, United States
| | - Andres Collazo
- Beckman Institute, CalTech, Pasadena, CA, 91125, United States
| | - Olivier George
- Department of Psychiatry, UC San Diego, La Jolla, CA, 92032, United States
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Stockhausen A, Rodriguez-Gatica JE, Schweihoff J, Schwarz MK, Kubitscheck U. Airy beam light sheet microscopy boosted by deep learning deconvolution. OPTICS EXPRESS 2023; 31:10918-10935. [PMID: 37157627 DOI: 10.1364/oe.485699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Common light sheet microscopy comes with a trade-off between light sheet width defining the optical sectioning and the usable field of view arising from the divergence of the illuminating Gaussian beam. To overcome this, low-diverging Airy beams have been introduced. Airy beams, however, exhibit side lobes degrading image contrast. Here, we constructed an Airy beam light sheet microscope, and developed a deep learning image deconvolution to remove the effects of the side lobes without knowledge of the point spread function. Using a generative adversarial network and high-quality training data, we significantly enhanced image contrast and improved the performance of a bicubic upscaling. We evaluated the performance with fluorescently labeled neurons in mouse brain tissue samples. We found that deep learning-based deconvolution was about 20-fold faster than the standard approach. The combination of Airy beam light sheet microscopy and deep learning deconvolution allows imaging large volumes rapidly and with high quality.
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40
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Kleven H, Reiten I, Blixhavn CH, Schlegel U, Øvsthus M, Papp EA, Puchades MA, Bjaalie JG, Leergaard TB, Bjerke IE. A neuroscientist's guide to using murine brain atlases for efficient analysis and transparent reporting. Front Neuroinform 2023; 17:1154080. [PMID: 36970659 PMCID: PMC10033636 DOI: 10.3389/fninf.2023.1154080] [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: 01/30/2023] [Accepted: 02/21/2023] [Indexed: 03/12/2023] Open
Abstract
Brain atlases are widely used in neuroscience as resources for conducting experimental studies, and for integrating, analyzing, and reporting data from animal models. A variety of atlases are available, and it may be challenging to find the optimal atlas for a given purpose and to perform efficient atlas-based data analyses. Comparing findings reported using different atlases is also not trivial, and represents a barrier to reproducible science. With this perspective article, we provide a guide to how mouse and rat brain atlases can be used for analyzing and reporting data in accordance with the FAIR principles that advocate for data to be findable, accessible, interoperable, and re-usable. We first introduce how atlases can be interpreted and used for navigating to brain locations, before discussing how they can be used for different analytic purposes, including spatial registration and data visualization. We provide guidance on how neuroscientists can compare data mapped to different atlases and ensure transparent reporting of findings. Finally, we summarize key considerations when choosing an atlas and give an outlook on the relevance of increased uptake of atlas-based tools and workflows for FAIR data sharing.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ingvild E. Bjerke
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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41
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Zhu J, Liu X, Xu J, Deng Y, Wang P, Liu Z, Yang Q, Li D, Yu T, Zhu D. A versatile vessel casting method for fine mapping of vascular networks using a hydrogel-based lipophilic dye solution. CELL REPORTS METHODS 2023; 3:100407. [PMID: 36936073 PMCID: PMC10014313 DOI: 10.1016/j.crmeth.2023.100407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/11/2022] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
Abstract
Efficient labeling of the vasculature is important for understanding the organization of vascular networks. Here, we propose VALID, a vessel-labeling method that enables visualization of vascular networks with tissue clearing and light-sheet microscopy. VALID transforms traditional lipophilic dye solution into hydrogel by introducing gelatin and restrains the dye aggregation, resulting in complete and uniform vessel-labeling patterns with high signal-to-background ratios. VALID also enhances the compatibility of lipophilic dyes with solvent-based tissue-clearing protocols, which was hard to achieve previously. Using VALID, we combined lipophilic dyes with solvent-based tissue-clearing techniques to perform 3D reconstructions of vasculature within mouse brain and spinal cord. We also employed VALID for 3D visualization and quantification of microvascular damage in a middle cerebral artery occlusion mouse model. VALID should provide a simple, cost-effective vessel-labeling protocol that would significantly widen the applications of lipophilic dyes in research on cerebrovascular complications.
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Affiliation(s)
- Jingtan Zhu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Xiaomei Liu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Jianyi Xu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yating Deng
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Pingfu Wang
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Zhang Liu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Qihang Yang
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Dongyu Li
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Tingting Yu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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Nonaka H, Mino T, Sakamoto S, Oh JH, Watanabe Y, Ishikawa M, Tsushima A, Amaike K, Kiyonaka S, Tamura T, Aricescu AR, Kakegawa W, Miura E, Yuzaki M, Hamachi I. Revisiting PFA-mediated tissue fixation chemistry: FixEL enables trapping of small molecules in the brain to visualize their distribution changes. Chem 2023; 9:523-540. [PMID: 38094901 PMCID: PMC7615374 DOI: 10.1016/j.chempr.2022.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Various small molecules have been used as functional probes for tissue imaging in medical diagnosis and pharmaceutical drugs for disease treatment. The spatial distribution, target selectivity, and diffusion/excretion kinetics of small molecules in structurally complicated specimens are critical for function. However, robust methods for precisely evaluating these parameters in the brain have been limited. Herein, we report a new method termed "fixation-driven chemical cross-linking of exogenous ligands (FixEL)," which traps and images exogenously administered molecules of interest (MOIs) in complex tissues. This method relies on protein-MOI interactions and chemical cross-linking of amine-tethered MOI with paraformaldehyde used for perfusion fixation. FixEL is used to obtain images of the distribution of the small molecules, which addresses selective/nonselective binding to proteins, time-dependent localization changes, and diffusion/retention kinetics of MOIs such as the scaffold of PET tracer derivatives or drug-like small molecules.
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Affiliation(s)
- Hiroshi Nonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - Takeharu Mino
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Jae Hoon Oh
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - Yu Watanabe
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Mamoru Ishikawa
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - Akihiro Tsushima
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Kazuma Amaike
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Shigeki Kiyonaka
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - A. Radu Aricescu
- Division of Structural Biology, University of Oxford, Oxford OX3 7BN, UK
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Wataru Kakegawa
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
- Department of Neurophysiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Eriko Miura
- Department of Neurophysiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Michisuke Yuzaki
- Department of Neurophysiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
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Bijoch Ł, Klos J, Pawłowska M, Wiśniewska J, Legutko D, Szachowicz U, Kaczmarek L, Beroun A. Whole-brain tracking of cocaine and sugar rewards processing. Transl Psychiatry 2023; 13:20. [PMID: 36683039 PMCID: PMC9868126 DOI: 10.1038/s41398-023-02318-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Natural rewards, such as food, and sex are appetitive stimuli available for animals in their natural environment. Similarly, addictive rewards such as drugs of abuse possess strong, positive valence, but their action relies on their pharmacological properties. Nevertheless, it is believed that both of these kinds of rewards activate similar brain circuitry. The present study aimed to discover which parts of the brain process the experience of natural and addictive rewards. To holistically address this question, we used a single-cell whole-brain imaging approach to find patterns of activation for acute and prolonged sucrose and cocaine exposure. We analyzed almost 400 brain structures and created a brain-wide map of specific, c-Fos-positive neurons engaged by these rewards. Acute but not prolonged sucrose exposure triggered a massive c-Fos expression throughout the brain. Cocaine exposure on the other hand potentiated c-Fos expression with prolonged use, engaging more structures than sucrose treatment. The functional connectivity analysis unraveled an increase in brain modularity after the initial exposure to both types of rewards. This modularity was increased after repeated cocaine, but not sucrose, intake. To check whether discrepancies between the processing of both types of rewards can be found on a cellular level, we further studied the nucleus accumbens, one of the most strongly activated brain structures by both sucrose and cocaine experience. We found a high overlap between natural and addictive rewards on the level of c-Fos expression. Electrophysiological measurements of cellular correlates of synaptic plasticity revealed that natural and addictive rewards alike induce the accumulation of silent synapses. These results strengthen the hypothesis that in the nucleus accumbens drugs of abuse cause maladaptive neuronal plasticity in the circuitry that typically processes natural rewards.
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Affiliation(s)
- Łukasz Bijoch
- grid.419305.a0000 0001 1943 2944Laboratory of Neuronal Plasticity, Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Klos
- grid.419305.a0000 0001 1943 2944Laboratory of Neuronal Plasticity, Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Monika Pawłowska
- grid.419305.a0000 0001 1943 2944Laboratory of Neurobiology, Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland ,grid.12847.380000 0004 1937 1290Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Justyna Wiśniewska
- grid.419305.a0000 0001 1943 2944Laboratory of Neuronal Plasticity, Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Diana Legutko
- grid.419305.a0000 0001 1943 2944Laboratory of Neurobiology, Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Urszula Szachowicz
- grid.419305.a0000 0001 1943 2944Laboratory of Neuronal Plasticity, Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Leszek Kaczmarek
- grid.419305.a0000 0001 1943 2944Laboratory of Neurobiology, Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Anna Beroun
- Laboratory of Neuronal Plasticity, Nencki-EMBL Center of Excellence for Neural Plasticity and Brain Disorders: BRAINCITY, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland.
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Zwang TJ, Bennett RE, Lysandrou M, Woost B, Zhang A, Lieber CM, Richardson DS, Hyman BT. Tissue libraries enable rapid determination of conditions that preserve antibody labeling in cleared mouse and human tissue. eLife 2023; 12:e84112. [PMID: 36656755 PMCID: PMC9889093 DOI: 10.7554/elife.84112] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/18/2023] [Indexed: 01/20/2023] Open
Abstract
Difficulty achieving complete, specific, and homogenous staining is a major bottleneck preventing the widespread use of tissue clearing techniques to image large volumes of human tissue. In this manuscript, we describe a procedure to rapidly design immunostaining protocols for antibody labeling of cleared brain tissue. We prepared libraries of 0.5-1.0 mm thick tissue sections that are fixed, pre-treated, and cleared via similar, but different procedures to optimize staining conditions for a panel of antibodies. Results from a library of mouse tissue correlate well with results from a similarly prepared library of human brain tissue, suggesting mouse tissue is an adequate substitute for protocol optimization. These data show that procedural differences do not influence every antibody-antigen pair in the same way, and minor changes can have deleterious effects, therefore, optimization should be conducted for each target. The approach outlined here will help guide researchers to successfully label a variety of targets, thus removing a major hurdle to accessing the rich 3D information available in large, cleared human tissue volumes.
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Affiliation(s)
- Theodore J Zwang
- Department of Neurology, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Harvard Medical SchoolBostonUnited States
- Massachusetts Alzheimer’s Disease Research CenterCharlestownUnited States
| | - Rachel E Bennett
- Department of Neurology, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Harvard Medical SchoolBostonUnited States
- Massachusetts Alzheimer’s Disease Research CenterCharlestownUnited States
| | - Maria Lysandrou
- Department of Neurology, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Benjamin Woost
- Department of Neurology, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Anqi Zhang
- Department of Chemical Engineering, Stanford UniversityStanfordUnited States
| | - Charles M Lieber
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Douglas S Richardson
- Department of Molecular and Cellular Biology and Harvard Center for Biological Imaging, Harvard UniversityCambridgeUnited States
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Harvard Medical SchoolBostonUnited States
- Massachusetts Alzheimer’s Disease Research CenterCharlestownUnited States
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Hedde PN, Le BT, Gomez EL, Duong L, Steele RE, Ahrar S. SPIM-Flow: An Integrated Light Sheet and Microfluidics Platform for Hydrodynamic Studies of Hydra. BIOLOGY 2023; 12:biology12010116. [PMID: 36671808 PMCID: PMC9856110 DOI: 10.3390/biology12010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Selective plane illumination microscopy (SPIM), or light sheet microscopy, is a powerful imaging approach. However, access to and interfacing microscopes with microfluidics have remained challenging. Complex interfacing with microfluidics has limited the SPIM's utility for studying the hydrodynamics of freely moving multicellular organisms. We developed SPIM-Flow, an inexpensive light sheet platform that enables easy integration with microfluidics. We used SPIM-Flow to investigate the hydrodynamics of a freely moving Hydra polyp via particle tracking in millimeter-sized chambers. Initial experiments across multiple animals, feeding on a chip (Artemia franciscana nauplii used as food), and baseline behaviors (tentacle swaying, elongation, and bending) indicated the organisms' health inside the system. Fluidics were used to investigate Hydra's response to flow. The results suggested that the animals responded to an established flow by bending and swaying their tentacles in the flow direction. Finally, using SPIM-Flow in a proof-of-concept experiment, the shear stress required to detach an animal from a surface was demonstrated. Our results demonstrated SPIM-Flow's utility for investigating the hydrodynamics of freely moving animals.
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Affiliation(s)
- Per Niklas Hedde
- Beckman Laser Institute and Medical Clinic, University of California Irvine, Irvine, CA 92612, USA
- Correspondence: (P.N.H.); (S.A.)
| | - Brian T. Le
- Department of Biomedical Engineering, CSU Long Beach, Long Beach, CA 90840, USA
| | - Erika L. Gomez
- Department of Biomedical Engineering, CSU Long Beach, Long Beach, CA 90840, USA
| | - Leora Duong
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Robert E. Steele
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Siavash Ahrar
- Department of Biomedical Engineering, CSU Long Beach, Long Beach, CA 90840, USA
- Department of Physics and Astronomy, University of California Irvine, Irvine, CA 92697, USA
- Correspondence: (P.N.H.); (S.A.)
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Song JY, Patton CD, Friedman R, Mahajan LS, Nordlicht R, Sayed R, Lipton ML. Hormonal contraceptives and the brain: A systematic review on 60 years of neuroimaging, EEG, and biochemical studies in humans and animals. Front Neuroendocrinol 2023; 68:101051. [PMID: 36577486 PMCID: PMC9898167 DOI: 10.1016/j.yfrne.2022.101051] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/26/2022]
Abstract
Hormonal contraception has been widely prescribed for decades. Although safety and efficacy are well-established, much uncertainty remains regarding brain effects of hormonal contraception. We systematically review human and animal studies on the brain effects of hormonal contraception which employed neuroimaging techniques such as MRI, PET and EEG, as well as animal studies which reported on neurotransmitter and other brain biochemical effects. We screened 1001 articles and ultimately extracted data from 70, comprising 51 human and 19 animal studies. Of note, there were no animal studies which employed structural or functional MRI, MRS or PET. In summary, our review shows hormonal contraceptive associations with changes in the brain have been documented. Many questions remain and more studies are needed to describe the effects of hormonal contraception on the brain.
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Affiliation(s)
- Joan Y Song
- The Gruss Magnetic Resonance Research Center, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA; Department of Radiology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA; The Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | | | - Renee Friedman
- The Gruss Magnetic Resonance Research Center, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Lakshmi S Mahajan
- The Gruss Magnetic Resonance Research Center, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Rachel Nordlicht
- The Gruss Magnetic Resonance Research Center, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Rahman Sayed
- The Gruss Magnetic Resonance Research Center, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Michael L Lipton
- The Gruss Magnetic Resonance Research Center, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA; Department of Radiology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA; The Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA.
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Wouterlood FG. Techniques to Render Dendritic Spines Visible in the Microscope. ADVANCES IN NEUROBIOLOGY 2023; 34:69-102. [PMID: 37962794 DOI: 10.1007/978-3-031-36159-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
A tiny detail visible on certain neurons at the limit of resolution in light microscopy went in 130 years of neuroscience research through a dazzling career from suspicious staining artifact to what we recognize today as a complex postsynaptic molecular machine: the dendritic spine.This chapter deals with techniques to make spines visible. The original technique, Golgi silver staining, is still being used today. Electron microscopy and automated field ion beam scanning electron microscopy are ultrahigh resolution techniques, albeit specialized. Other methods are intracellular injection, uptake of dyes, and recently the exploitation of genetically modified animals in which certain neurons express fluorescent protein in all their processes, including the nooks and crannies of their dendritic spines.
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Affiliation(s)
- Floris G Wouterlood
- Department of Anatomy & Neurosciences, Amsterdam UMC, Amsterdam, The Netherlands
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Cao Y, Lee S, Kim K, Kang SH. Minimizing the Optical Illusion of Nanoparticles in Single Cells Using Four-Dimensional Cuboid Multiangle Illumination-Based Light-Sheet Super-Resolution Imaging. Anal Chem 2022; 94:17877-17884. [PMID: 36509731 DOI: 10.1021/acs.analchem.2c03729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although light-sheet-based super-resolution microscopy is an excellent detection technique for biological samples because of minimal photodamage, uneven light paths due to solid-angle illumination limits it, resulting in an optical illusion. Furthermore, the optical illusion limits the observations of individual molecules in diffraction. In this study, a four-dimensional cuboid multiangle illumination-based light-sheet super-resolution (4D CMLS) imaging system was developed to minimize optical illusions in cells. The lab-built 4D CMLS imaging system was integrated with total internal reflection fluorescence and a differential interference contrast microscope. A specially designed rotatable cuboid prism simply overcame the optical illusion by rotating a specimen on the prism to change the direction of light coming from an illumination lens. 4D CMLS reconstructed images of nanoparticles of different sizes were acquired in multi-illumination angles of 0°, 90°, 180°, and 270°. Additionally, a 4D multiangle illumination-based algorithm was created to select the optimal illumination angle by combining three-dimensional super-resolution imaging with multiangle observation, even in the presence of obstacles. The 4D CMLS imaging method demonstrates the in-depth 4D observation of samples at an optimum angle that can be used in various applications, such as single-molecule and subcellular organelle observations in single cells at subdiffraction limit resolutions that describe the scenario of nature.
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Affiliation(s)
- Yingying Cao
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Seungah Lee
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Kyungsoo Kim
- Department of Applied Mathematics, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Seong Ho Kang
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea.,Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
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Bhatia HS, Brunner AD, Öztürk F, Kapoor S, Rong Z, Mai H, Thielert M, Ali M, Al-Maskari R, Paetzold JC, Kofler F, Todorov MI, Molbay M, Kolabas ZI, Negwer M, Hoeher L, Steinke H, Dima A, Gupta B, Kaltenecker D, Caliskan ÖS, Brandt D, Krahmer N, Müller S, Lichtenthaler SF, Hellal F, Bechmann I, Menze B, Theis F, Mann M, Ertürk A. Spatial proteomics in three-dimensional intact specimens. Cell 2022; 185:5040-5058.e19. [PMID: 36563667 DOI: 10.1016/j.cell.2022.11.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/13/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022]
Abstract
Spatial molecular profiling of complex tissues is essential to investigate cellular function in physiological and pathological states. However, methods for molecular analysis of large biological specimens imaged in 3D are lacking. Here, we present DISCO-MS, a technology that combines whole-organ/whole-organism clearing and imaging, deep-learning-based image analysis, robotic tissue extraction, and ultra-high-sensitivity mass spectrometry. DISCO-MS yielded proteome data indistinguishable from uncleared samples in both rodent and human tissues. We used DISCO-MS to investigate microglia activation along axonal tracts after brain injury and characterized early- and late-stage individual amyloid-beta plaques in a mouse model of Alzheimer's disease. DISCO-bot robotic sample extraction enabled us to study the regional heterogeneity of immune cells in intact mouse bodies and aortic plaques in a complete human heart. DISCO-MS enables unbiased proteome analysis of preclinical and clinical tissues after unbiased imaging of entire specimens in 3D, identifying diagnostic and therapeutic opportunities for complex diseases. VIDEO ABSTRACT.
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Affiliation(s)
- Harsharan Singh Bhatia
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Andreas-David Brunner
- Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Str. 65, D-88400 Biberach Riss, Germany
| | - Furkan Öztürk
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Saketh Kapoor
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Zhouyi Rong
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Hongcheng Mai
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Marvin Thielert
- Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Mayar Ali
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Graduate School of Neuroscience (GSN), 82152 Munich, Germany
| | - Rami Al-Maskari
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany
| | - Johannes Christian Paetzold
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany; Biomedical Image Analysis Group, Department of Computing, Imperial College London, London SW7 2AZ, UK
| | - Florian Kofler
- Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany; Helmholtz AI, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Neuroradiology, Klinikum rechts der Isar, 81675 Munich, Germany
| | - Mihail Ivilinov Todorov
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Muge Molbay
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Zeynep Ilgin Kolabas
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Graduate School of Neuroscience (GSN), 82152 Munich, Germany
| | - Moritz Negwer
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Luciano Hoeher
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Hanno Steinke
- Institute of Anatomy, University of Leipzig, 04109 Leipzig, Germany
| | - Alina Dima
- Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany
| | - Basavdatta Gupta
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Doris Kaltenecker
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Institute for Diabetes and Cancer, Helmholz Zentrum München, 85764 Neuherberg, Germany
| | - Özüm Sehnaz Caliskan
- Institute for Diabetes and Obesity, Helmholz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research, Helmholz Zentrum München, 85764 Neuherberg, Germany
| | - Daniel Brandt
- Institute for Diabetes and Obesity, Helmholz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research, Helmholz Zentrum München, 85764 Neuherberg, Germany
| | - Natalie Krahmer
- Institute for Diabetes and Obesity, Helmholz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research, Helmholz Zentrum München, 85764 Neuherberg, Germany
| | - Stephan Müller
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Stefan Frieder Lichtenthaler
- Graduate School of Neuroscience (GSN), 82152 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Farida Hellal
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Ingo Bechmann
- Institute of Anatomy, University of Leipzig, 04109 Leipzig, Germany
| | - Bjoern Menze
- Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany; Department for Quantitative Biomedicine, University of Zurich, 8006 Zurich, Switzerland
| | - Fabian Theis
- Institute of Computational Biology, Helmholz Zentrum München, 85764 Neuherberg, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany; Department of Mathematics, Technical University of Munich, 85748 Garching, Germany
| | - Matthias Mann
- Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Ali Ertürk
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Graduate School of Neuroscience (GSN), 82152 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany.
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50
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Practical considerations for quantitative light sheet fluorescence microscopy. Nat Methods 2022; 19:1538-1549. [PMID: 36266466 DOI: 10.1038/s41592-022-01632-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/31/2022] [Indexed: 12/25/2022]
Abstract
Fluorescence microscopy has evolved from a purely observational tool to a platform for quantitative, hypothesis-driven research. As such, the demand for faster and less phototoxic imaging modalities has spurred a rapid growth in light sheet fluorescence microscopy (LSFM). By restricting the excitation to a thin plane, LSFM reduces the overall light dose to a specimen while simultaneously improving image contrast. However, the defining characteristics of light sheet microscopes subsequently warrant unique considerations in their use for quantitative experiments. In this Perspective, we outline many of the pitfalls in LSFM that can compromise analysis and confound interpretation. Moreover, we offer guidance in addressing these caveats when possible. In doing so, we hope to provide a useful resource for life scientists seeking to adopt LSFM to quantitatively address complex biological hypotheses.
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