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Yu T, Zhong X, Yang Q, Gao C, Chen W, Liu X, Liu Z, Zhu T, Li D, Fei P, Chen Z, Gu Z, Zhu D. On-chip clearing for live imaging of 3D cell cultures. BIOMEDICAL OPTICS EXPRESS 2023; 14:3003-3017. [PMID: 37342722 PMCID: PMC10278639 DOI: 10.1364/boe.489219] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/07/2023] [Accepted: 05/07/2023] [Indexed: 06/23/2023]
Abstract
Three-dimensional (3D) cell cultures provide an important model for various biological studies by bridging the gap between two-dimensional (2D) cell cultures and animal tissues. Microfluidics has recently provided controllable platforms for handling and analyzing 3D cell cultures. However, on-chip imaging of 3D cell cultures within microfluidic devices is hindered by the inherent high scattering of 3D tissues. Tissue optical clearing techniques have been used to address this concern but remain limited to fixed samples. As such, there is still a need for an on-chip clearing method for imaging live 3D cell cultures. Here, to achieve on-chip clearing for live imaging of 3D cell cultures, we conceived a simple microfluidic device by integrating a U-shaped concave for culture, parallel channels with micropillars, and differentiated surface treatment to enable on-chip 3D cell culture, clearing, and live imaging with minimal disturbance. The on-chip tissue clearing increased the imaging performance of live 3D spheroids with no influence on cell viability or spheroid proliferation and demonstrated robust compatibility with several commonly used cell probes. It allowed dynamic tracking of lysosomes in live tumor spheroids and enabled quantitative analysis of their motility in the deeper layer. Our proposed method of on-chip clearing for live imaging of 3D cell cultures provides an alternative for dynamic monitoring of deep tissue on a microfluidic device and has the potential to be used in 3D culture-based assays for high-throughput applications.
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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
| | - Xiang Zhong
- 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
| | - Chao Gao
- 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
| | - Wenyue Chen
- 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
| | - Xiang Liu
- 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
| | - Zhang Liu
- 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
| | - Tingting Zhu
- Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dongyu Li
- Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Peng Fei
- Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zaozao Chen
- 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
| | - 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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Dyer L, Parker A, Paphiti K, Sanderson J. Lightsheet Microscopy. Curr Protoc 2022; 2:e448. [PMID: 35838628 DOI: 10.1002/cpz1.448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this paper, we review lightsheet (selective plane illumination) microscopy for mouse developmental biologists. There are different means of forming the illumination sheet, and we discuss these. We explain how we introduced the lightsheet microscope economically into our core facility and present our results on fixed and living samples. We also describe methods of clearing fixed samples for three-dimensional imaging and discuss the various means of preparing samples with particular reference to mouse cilia, adipose spheroids, and cochleae. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Laura Dyer
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Andrew Parker
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Keanu Paphiti
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
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Susaki EA, Takasato M. Perspective: Extending the Utility of Three-Dimensional Organoids by Tissue Clearing Technologies. Front Cell Dev Biol 2021; 9:679226. [PMID: 34195197 PMCID: PMC8236633 DOI: 10.3389/fcell.2021.679226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 01/06/2023] Open
Abstract
An organoid, a self-organizing organ-like tissue developed from stem cells, can exhibit a miniaturized three-dimensional (3D) structure and part of the physiological functions of the original organ. Due to the reproducibility of tissue complexity and ease of handling, organoids have replaced real organs and animals for a variety of uses, such as investigations of the mechanisms of organogenesis and disease onset, and screening of drug effects and/or toxicity. The recent advent of tissue clearing and 3D imaging techniques have great potential contributions to organoid studies by allowing the collection and analysis of 3D images of whole organoids with a reasonable throughput and thus can expand the means of examining the 3D architecture, cellular components, and variability among organoids. Genetic and histological cell-labeling methods, together with organoid clearing, also allow visualization of critical structures and cellular components within organoids. The collected 3D data may enable image analysis to quantitatively assess structures within organoids and sensitively/effectively detect abnormalities caused by perturbations. These capabilities of tissue/organoid clearing and 3D imaging techniques not only extend the utility of organoids in basic biology but can also be applied for quality control of clinical organoid production and large-scale drug screening.
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Affiliation(s)
- Etsuo A. Susaki
- Department of Biochemistry and Systems Biomedicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Minoru Takasato
- Laboratory for Human Organogenesis, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Laboratory of Molecular Cell Biology and Development, Department of Animal Development and Physiology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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Diosdi A, Hirling D, Kovacs M, Toth T, Harmati M, Koos K, Buzas K, Piccinini F, Horvath P. A quantitative metric for the comparative evaluation of optical clearing protocols for 3D multicellular spheroids. Comput Struct Biotechnol J 2021; 19:1233-1243. [PMID: 33717421 PMCID: PMC7907228 DOI: 10.1016/j.csbj.2021.01.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/19/2021] [Accepted: 01/23/2021] [Indexed: 12/18/2022] Open
Abstract
3D multicellular spheroids quickly emerged as in vitro models because they represent the in vivo tumor environment better than standard 2D cell cultures. However, with current microscopy technologies, it is difficult to visualize individual cells in the deeper layers of 3D samples mainly because of limited light penetration and scattering. To overcome this problem several optical clearing methods have been proposed but defining the most appropriate clearing approach is an open issue due to the lack of a gold standard metric. Here, we propose a guideline for 3D light microscopy imaging to achieve single-cell resolution. The guideline includes a validation experiment focusing on five optical clearing protocols. We review and compare seven quality metrics which quantitatively characterize the imaging quality of spheroids. As a test environment, we have created and shared a large 3D dataset including approximately hundred fluorescently stained and optically cleared spheroids. Based on the results we introduce the use of a novel quality metric as a promising method to serve as a gold standard, applicable to compare optical clearing protocols, and decide on the most suitable one for a particular experiment.
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Affiliation(s)
- Akos Diosdi
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), H-6726 Szeged, Hungary
- Doctoral School of Biology, University of Szeged, H-6726 Szeged, Hungary
| | - Dominik Hirling
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), H-6726 Szeged, Hungary
- Doctoral School of Computer Science, University of Szeged, H-6701 Szeged, Hungary
| | - Maria Kovacs
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), H-6726 Szeged, Hungary
| | - Timea Toth
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), H-6726 Szeged, Hungary
- Doctoral School of Biology, University of Szeged, H-6726 Szeged, Hungary
| | - Maria Harmati
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), H-6726 Szeged, Hungary
| | - Krisztian Koos
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), H-6726 Szeged, Hungary
| | - Krisztina Buzas
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), H-6726 Szeged, Hungary
- Department of Immunology, Faculty of Medicine, Faculty of Science and Informatics, University of Szeged, H-6720 Szeged, Hungary
| | - Filippo Piccinini
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Via Piero Maroncelli 40, I-47014 Meldola, FC, Italy
| | - Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), H-6726 Szeged, Hungary
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014 Helsinki, Finland
- Single-Cell Technologies Ltd., H-6726 Szeged, Hungary
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Influence of ClearT and ClearT2 Agitation Conditions in the Fluorescence Imaging of 3D Spheroids. Int J Mol Sci 2020; 22:ijms22010266. [PMID: 33383886 PMCID: PMC7796078 DOI: 10.3390/ijms22010266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/25/2020] [Accepted: 12/26/2020] [Indexed: 11/16/2022] Open
Abstract
3D tumor spheroids have arisen in the last years as potent tools for the in vitro screening of novel anticancer therapeutics. Nevertheless, to increase the reproducibility and predictability of the data originated from the spheroids it is still necessary to develop or optimize the techniques used for spheroids’ physical and biomolecular characterization. Fluorescence microscopy, such as confocal laser scanning microscopy (CLSM), is a tool commonly used by researchers to characterize spheroids structure and the antitumoral effect of novel therapeutics. However, its application in spheroids’ analysis is hindered by the limited light penetration in thick samples. For this purpose, optical clearing solutions have been explored to increase the spheroids’ transparency by reducing the light scattering. In this study, the influence of agitation conditions (i.e., static, horizontal agitation, and rotatory agitation) on the ClearT and ClearT2 methods’ clearing efficacy and tumor spheroids’ imaging by CLSM was characterized. The obtained results demonstrate that the ClearT method results in the improved imaging of the spheroids interior, whereas the ClearT2 resulted in an increased propidium iodide mean fluorescence intensity as well as a higher signal depth in the Z-axis. Additionally, for both methods, the best clearing results were obtained for the spheroids treated under the rotatory agitation. In general, this work provides new insights on the ClearT and ClearT2 clearing methodologies and their utilization for improving the reproducibility of the data obtained through the CLSM, such as the analysis of the cell death in response to therapeutics administration.
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Nürnberg E, Vitacolonna M, Klicks J, von Molitor E, Cesetti T, Keller F, Bruch R, Ertongur-Fauth T, Riedel K, Scholz P, Lau T, Schneider R, Meier J, Hafner M, Rudolf R. Routine Optical Clearing of 3D-Cell Cultures: Simplicity Forward. Front Mol Biosci 2020; 7:20. [PMID: 32154265 PMCID: PMC7046628 DOI: 10.3389/fmolb.2020.00020] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/04/2020] [Indexed: 12/11/2022] Open
Abstract
Three-dimensional cell cultures, such as spheroids and organoids, serve as increasingly important models in fundamental and applied research and start to be used for drug screening purposes. Optical tissue clearing procedures are employed to enhance visualization of fluorescence-stained organs, tissues, and three-dimensional cell cultures. To get a more systematic overview about the effects and applicability of optical tissue clearing on three-dimensional cell cultures, we compared six different clearing/embedding protocols on seven types of spheroid- and chip-based three-dimensional cell cultures of approximately 300 μm in size that were stained with nuclear dyes, immunofluorescence, cell trackers, and cyan fluorescent protein. Subsequent whole mount confocal microscopy and semi-automated image analysis were performed to quantify the effects. Quantitative analysis included fluorescence signal intensity and signal-to-noise ratio as a function of z-depth as well as segmentation and counting of nuclei and immunopositive cells. In general, these analyses revealed five key points, which largely confirmed current knowledge and were quantified in this study. First, there was a massive variability of effects of different clearing protocols on sample transparency and shrinkage as well as on dye quenching. Second, all tested clearing protocols worked more efficiently on samples prepared with one cell type than on co-cultures. Third, z-compensation was imperative to minimize variations in signal-to-noise ratio. Fourth, a combination of sample-inherent cell density, sample shrinkage, uniformity of signal-to-noise ratio, and image resolution had a strong impact on data segmentation, cell counts, and relative numbers of immunofluorescence-positive cells. Finally, considering all mentioned aspects and including a wish for simplicity and speed of protocols - in particular, for screening purposes - clearing with 88% Glycerol appeared to be the most promising option amongst the ones tested.
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Affiliation(s)
- Elina Nürnberg
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany.,Zentralinstitut für Seelische Gesundheit, Department of Translational Brain Research, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Mario Vitacolonna
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Julia Klicks
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Elena von Molitor
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Tiziana Cesetti
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Florian Keller
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Roman Bruch
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | | | | | | | - Thorsten Lau
- Zentralinstitut für Seelische Gesundheit, Department of Translational Brain Research, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Julia Meier
- TIP Oncology, Merck Healthcare KGaA, Darmstadt, Germany
| | - Mathias Hafner
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Rüdiger Rudolf
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
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