1
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Sonmez UM, Frey N, LeDuc PR, Minden JS. Fly Me to the Micron: Microtechnologies for Drosophila Research. Annu Rev Biomed Eng 2024; 26:441-473. [PMID: 38959386 DOI: 10.1146/annurev-bioeng-050423-054647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Multicellular model organisms, such as Drosophila melanogaster (fruit fly), are frequently used in a myriad of biological research studies due to their biological significance and global standardization. However, traditional tools used in these studies generally require manual handling, subjective phenotyping, and bulk treatment of the organisms, resulting in laborious experimental protocols with limited accuracy. Advancements in microtechnology over the course of the last two decades have allowed researchers to develop automated, high-throughput, and multifunctional experimental tools that enable novel experimental paradigms that would not be possible otherwise. We discuss recent advances in microtechnological systems developed for small model organisms using D. melanogaster as an example. We critically analyze the state of the field by comparing the systems produced for different applications. Additionally, we suggest design guidelines, operational tips, and new research directions based on the technical and knowledge gaps in the literature. This review aims to foster interdisciplinary work by helping engineers to familiarize themselves with model organisms while presenting the most recent advances in microengineering strategies to biologists.
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Affiliation(s)
- Utku M Sonmez
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA;
- Current affiliation: Department of Neuroscience, Scripps Research, San Diego, California, USA
- Current affiliation: Department of NanoEngineering, University of California San Diego, La Jolla, California, USA
| | - Nolan Frey
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA;
| | - Philip R LeDuc
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA;
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Jonathan S Minden
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA;
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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2
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Way GP, Sailem H, Shave S, Kasprowicz R, Carragher NO. Evolution and impact of high content imaging. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:292-305. [PMID: 37666456 DOI: 10.1016/j.slasd.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/09/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023]
Abstract
The field of high content imaging has steadily evolved and expanded substantially across many industry and academic research institutions since it was first described in the early 1990's. High content imaging refers to the automated acquisition and analysis of microscopic images from a variety of biological sample types. Integration of high content imaging microscopes with multiwell plate handling robotics enables high content imaging to be performed at scale and support medium- to high-throughput screening of pharmacological, genetic and diverse environmental perturbations upon complex biological systems ranging from 2D cell cultures to 3D tissue organoids to small model organisms. In this perspective article the authors provide a collective view on the following key discussion points relevant to the evolution of high content imaging: • Evolution and impact of high content imaging: An academic perspective • Evolution and impact of high content imaging: An industry perspective • Evolution of high content image analysis • Evolution of high content data analysis pipelines towards multiparametric and phenotypic profiling applications • The role of data integration and multiomics • The role and evolution of image data repositories and sharing standards • Future perspective of high content imaging hardware and software.
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Affiliation(s)
- Gregory P Way
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Heba Sailem
- School of Cancer and Pharmaceutical Sciences, King's College London, UK
| | - Steven Shave
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Rd, Stevenage SG1 2NY, UK; Edinburgh Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, UK
| | - Richard Kasprowicz
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Rd, Stevenage SG1 2NY, UK
| | - Neil O Carragher
- Edinburgh Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, UK.
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3
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Burton EA, Burgess HA. A Critical Review of Zebrafish Neurological Disease Models-2. Application: Functional and Neuroanatomical Phenotyping Strategies and Chemical Screens. OXFORD OPEN NEUROSCIENCE 2022; 2:kvac019. [PMID: 37637775 PMCID: PMC10455049 DOI: 10.1093/oons/kvac019] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/28/2022] [Indexed: 08/29/2023]
Abstract
Extensive phylogenetic conservation of molecular pathways and neuroanatomical structures, associated with efficient methods for genetic modification, have been exploited increasingly to generate zebrafish models of human disease. A range of powerful approaches can be deployed to analyze these models with the ultimate goal of elucidating pathogenic mechanisms and accelerating efforts to find effective treatments. Unbiased neurobehavioral assays can provide readouts that parallel clinical abnormalities found in patients, although some of the most useful assays quantify responses that are not routinely evaluated clinically, and differences between zebrafish and human brains preclude expression of the full range of neurobehavioral abnormalities seen in disease. Imaging approaches that use fluorescent reporters and standardized brain atlases coupled with quantitative measurements of brain structure offer an unbiased means to link experimental manipulations to changes in neural architecture. Together, quantitative structural and functional analyses allow dissection of the cellular and physiological basis underlying neurological phenotypes. These approaches can be used as outputs in chemical modifier screens, which provide a major opportunity to exploit zebrafish models to identify small molecule modulators of pathophysiology that may be informative for understanding disease mechanisms and possible therapeutic approaches.
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Affiliation(s)
- Edward A Burton
- Pittsburgh Institute of Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Geriatric Research, Education, and Clinical Center, Pittsburgh VA Healthcare System, Pittsburgh, PA 15240, USA
| | - Harold A Burgess
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
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4
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Wlodkowic D, Jansen M. High-throughput screening paradigms in ecotoxicity testing: Emerging prospects and ongoing challenges. CHEMOSPHERE 2022; 307:135929. [PMID: 35944679 DOI: 10.1016/j.chemosphere.2022.135929] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/09/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
The rapidly increasing number of new production chemicals coupled with stringent implementation of global chemical management programs necessities a paradigm shift towards boarder uses of low-cost and high-throughput ecotoxicity testing strategies as well as deeper understanding of cellular and sub-cellular mechanisms of ecotoxicity that can be used in effective risk assessment. The latter will require automated acquisition of biological data, new capabilities for big data analysis as well as computational simulations capable of translating new data into in vivo relevance. However, very few efforts have been so far devoted into the development of automated bioanalytical systems in ecotoxicology. This is in stark contrast to standardized and high-throughput chemical screening and prioritization routines found in modern drug discovery pipelines. As a result, the high-throughput and high-content data acquisition in ecotoxicology is still in its infancy with limited examples focused on cell-free and cell-based assays. In this work we outline recent developments and emerging prospects of high-throughput bioanalytical approaches in ecotoxicology that reach beyond in vitro biotests. We discuss future importance of automated quantitative data acquisition for cell-free, cell-based as well as developments in phytotoxicity and in vivo biotests utilizing small aquatic model organisms. We also discuss recent innovations such as organs-on-a-chip technologies and existing challenges for emerging high-throughput ecotoxicity testing strategies. Lastly, we provide seminal examples of the small number of successful high-throughput implementations that have been employed in prioritization of chemicals and accelerated environmental risk assessment.
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Affiliation(s)
- Donald Wlodkowic
- The Neurotox Lab, School of Science, RMIT University, Melbourne, VIC, 3083, Australia.
| | - Marcus Jansen
- LemnaTec GmbH, Nerscheider Weg 170, 52076, Aachen, Germany
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5
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6
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Abstract
Heart disease is the leading cause of death worldwide. Despite decades of research, most heart pathologies have limited treatments, and often the only curative approach is heart transplantation. Thus, there is an urgent need to develop new therapeutic approaches for treating cardiac diseases. Animal models that reproduce the human pathophysiology are essential to uncovering the biology of diseases and discovering therapies. Traditionally, mammals have been used as models of cardiac disease, but the cost of generating and maintaining new models is exorbitant, and the studies have very low throughput. In the last decade, the zebrafish has emerged as a tractable model for cardiac diseases, owing to several characteristics that made this animal popular among developmental biologists. Zebrafish fertilization and development are external; embryos can be obtained in high numbers, are cheap and easy to maintain, and can be manipulated to create new genetic models. Moreover, zebrafish exhibit an exceptional ability to regenerate their heart after injury. This review summarizes 25 years of research using the zebrafish to study the heart, from the classical forward screenings to the contemporary methods to model mutations found in patients with cardiac disease. We discuss the advantages and limitations of this model organism and introduce the experimental approaches exploited in zebrafish, including forward and reverse genetics and chemical screenings. Last, we review the models used to induce cardiac injury and essential ideas derived from studying natural regeneration. Studies using zebrafish have the potential to accelerate the discovery of new strategies to treat cardiac diseases.
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Affiliation(s)
- Juan Manuel González-Rosa
- Cardiovascular Research Center, Massachusetts General Hospital Research Institute, Harvard Medical School, Charlestown, MA
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7
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Chi Z, Xu Q, Ai N, Ge W. Design and Implementation of an Automatic Batch Microinjection System for Zebrafish Larvae. IEEE Robot Autom Lett 2022. [DOI: 10.1109/lra.2022.3143286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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8
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Otterstrom JJ, Lubin A, Payne EM, Paran Y. Technologies bringing young Zebrafish from a niche field to the limelight. SLAS Technol 2022; 27:109-120. [PMID: 35058207 DOI: 10.1016/j.slast.2021.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Fundamental life science and pharmaceutical research are continually striving to provide physiologically relevant context for their biological studies. Zebrafish present an opportunity for high-content screening (HCS) to bring a true in vivo model system to screening studies. Zebrafish embryos and young larvae are an economical, human-relevant model organism that are amenable to both genetic engineering and modification, and direct inspection via microscopy. The use of these organisms entails unique challenges that new technologies are overcoming, including artificial intelligence (AI). In this perspective article, we describe the state-of-the-art in terms of automated sample handling, imaging, and data analysis with zebrafish during early developmental stages. We highlight advances in orienting the embryos, including the use of robots, microfluidics, and creative multi-well plate solutions. Analyzing the micrographs in a fast, reliable fashion that maintains the anatomical context of the fluorescently labeled cells is a crucial step. Existing software solutions range from AI-driven commercial solutions to bespoke analysis algorithms. Deep learning appears to be a critical tool that researchers are only beginning to apply, but already facilitates many automated steps in the experimental workflow. Currently, such work has permitted the cellular quantification of multiple cell types in vivo, including stem cell responses to stress and drugs, neuronal myelination and macrophage behavior during inflammation and infection. We evaluate pro and cons of proprietary versus open-source methodologies for combining technologies into fully automated workflows of zebrafish studies. Zebrafish are poised to charge into HCS with ever-greater presence, bringing a new level of physiological context.
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Affiliation(s)
| | - Alexandra Lubin
- Research Department of Hematology, Cancer Institute, University College London, London, UK
| | - Elspeth M Payne
- Research Department of Hematology, Cancer Institute, University College London, London, UK
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9
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Ruiz OE, Samms KM, Eisenhoffer GT. A protocol to evaluate epithelial regeneration after inducing cell loss in zebrafish larvae. STAR Protoc 2022; 3:101073. [PMID: 35036954 PMCID: PMC8749296 DOI: 10.1016/j.xpro.2021.101073] [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] [Indexed: 12/03/2022] Open
Abstract
Epithelial tissues sustain barrier function by removing and replacing aberrant or unfit cells. Here, we describe approaches to evaluate epithelial restorative capacity after inducing cell loss in zebrafish larvae. We provide details to quantify morphological changes to the tail fin epithelium after cell loss, and instructions to interrogate changes in gene expression and proliferation associated with replacement of the lost cells. Together, this approach establishes an in vivo vertebrate model for the rapid assessment of molecular pathways controlling epithelial regeneration. For complete details on the use and execution of this profile, please refer to Wurster et al. (2021). Evaluation of epithelial restorative capacity after cell loss in zebrafish larvae Quantification of morphological changes related to cell loss in the tail fin epithelium Instructions to interrogate changes in gene expression after induced cell loss Steps to assess proliferation associated with replacement of the lost cells
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Affiliation(s)
- Oscar E Ruiz
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krystin M Samms
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George T Eisenhoffer
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Genetics and Epigenetics Graduate Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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10
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Zhang KS, Nadkarni AV, Paul R, Martin AM, Tang SKY. Microfluidic Surgery in Single Cells and Multicellular Systems. Chem Rev 2022; 122:7097-7141. [PMID: 35049287 DOI: 10.1021/acs.chemrev.1c00616] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Microscale surgery on single cells and small organisms has enabled major advances in fundamental biology and in engineering biological systems. Examples of applications range from wound healing and regeneration studies to the generation of hybridoma to produce monoclonal antibodies. Even today, these surgical operations are often performed manually, but they are labor intensive and lack reproducibility. Microfluidics has emerged as a powerful technology to control and manipulate cells and multicellular systems at the micro- and nanoscale with high precision. Here, we review the physical and chemical mechanisms of microscale surgery and the corresponding design principles, applications, and implementations in microfluidic systems. We consider four types of surgical operations: (1) sectioning, which splits a biological entity into multiple parts, (2) ablation, which destroys part of an entity, (3) biopsy, which extracts materials from within a living cell, and (4) fusion, which joins multiple entities into one. For each type of surgery, we summarize the motivating applications and the microfluidic devices developed. Throughout this review, we highlight existing challenges and opportunities. We hope that this review will inspire scientists and engineers to continue to explore and improve microfluidic surgical methods.
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Affiliation(s)
- Kevin S Zhang
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ambika V Nadkarni
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, United States
| | - Rajorshi Paul
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Adrian M Martin
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Sindy K Y Tang
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
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11
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Qian C, Tong M, Yu X, Zhuang S. CNN-based visual processing approach for biological sample microinjection systems. Neurocomputing 2021. [DOI: 10.1016/j.neucom.2021.06.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Lubin A, Otterstrom J, Hoade Y, Bjedov I, Stead E, Whelan M, Gestri G, Paran Y, Payne E. A versatile, automated and high-throughput drug screening platform for zebrafish embryos. Biol Open 2021; 10:bio058513. [PMID: 34472582 PMCID: PMC8430230 DOI: 10.1242/bio.058513] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/28/2021] [Indexed: 12/29/2022] Open
Abstract
Zebrafish provide a unique opportunity for drug screening in living animals, with the fast-developing, transparent embryos allowing for relatively high-throughput, microscopy-based screens. However, the limited availability of rapid, flexible imaging and analysis platforms has limited the use of zebrafish in drug screens. We have developed an easy-to-use, customisable automated screening procedure suitable for high-throughput phenotype-based screens of live zebrafish. We utilised the WiScan® Hermes High Content Imaging System to rapidly acquire brightfield and fluorescent images of embryos, and the WiSoft® Athena Zebrafish Application for analysis, which harnesses an Artificial Intelligence-driven algorithm to automatically detect fish in brightfield images, identify anatomical structures, partition the animal into regions and exclusively select the desired side-oriented fish. Our initial validation combined structural analysis with fluorescence images to enumerate GFP-tagged haematopoietic stem and progenitor cells in the tails of embryos, which correlated with manual counts. We further validated this system to assess the effects of genetic mutations and X-ray irradiation in high content using a wide range of assays. Further, we performed simultaneous analysis of multiple cell types using dual fluorophores in high throughput. In summary, we demonstrate a broadly applicable and rapidly customisable platform for high-content screening in zebrafish. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Alexandra Lubin
- Research Department of Haematology, Cancer Institute, University College London, London WC1E 6DD, UK
| | | | - Yvette Hoade
- Research Department of Haematology, Cancer Institute, University College London, London WC1E 6DD, UK
| | - Ivana Bjedov
- Research Department of Cancer Biology, Cancer Institute, University College London, London WC1E 6DD, UK
| | - Eleanor Stead
- Research Department of Cancer Biology, Cancer Institute, University College London, London WC1E 6DD, UK
| | - Matthew Whelan
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Gaia Gestri
- Department of Cell and Developmental Biology, University College London, London WC1E 6AR, UK
| | - Yael Paran
- IDEA Bio-Medical Ltd., Rehovot 76705, Israel
| | - Elspeth Payne
- Research Department of Haematology, Cancer Institute, University College London, London WC1E 6DD, UK
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13
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Han X, Su Y, White H, O'Neill KM, Morgan NY, Christensen R, Potarazu D, Vishwasrao HD, Xu S, Sun Y, Huang SY, Moyle MW, Dai Q, Pommier Y, Giniger E, Albrecht DR, Probst R, Shroff H. A polymer index-matched to water enables diverse applications in fluorescence microscopy. LAB ON A CHIP 2021; 21:1549-1562. [PMID: 33629685 PMCID: PMC8058278 DOI: 10.1039/d0lc01233e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We demonstrate diffraction-limited and super-resolution imaging through thick layers (tens-hundreds of microns) of BIO-133, a biocompatible, UV-curable, commercially available polymer with a refractive index (RI) matched to water. We show that cells can be directly grown on BIO-133 substrates without the need for surface passivation and use this capability to perform extended time-lapse volumetric imaging of cellular dynamics 1) at isotropic resolution using dual-view light-sheet microscopy, and 2) at super-resolution using instant structured illumination microscopy. BIO-133 also enables immobilization of 1) Drosophila tissue, allowing us to track membrane puncta in pioneer neurons, and 2) Caenorhabditis elegans, which allows us to image and inspect fine neural structure and to track pan-neuronal calcium activity over hundreds of volumes. Finally, BIO-133 is compatible with other microfluidic materials, enabling optical and chemical perturbation of immobilized samples, as we demonstrate by performing drug and optogenetic stimulation on cells and C. elegans.
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Affiliation(s)
- Xiaofei Han
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA. and Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA. and Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hamilton White
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA. and Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Kate M O'Neill
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA and Institute for Physical Science and Technology, University of Maryland College Park, College Park, MD 20742, USA
| | - Nicole Y Morgan
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan Christensen
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Deepika Potarazu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen Xu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Yilun Sun
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shar-Yin Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark W Moyle
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward Giniger
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dirk R Albrecht
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA. and Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Roland Probst
- ACUITYnano, Innovation in Biomedical Imaging, North Bethesda, MD 20850, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA. and Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA and Marine Biological Laboratory Fellows Program, Woods Hole, MA 02543, USA
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14
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Haney MG, Wimsett M, Liu C, Blackburn JS. Protocol for rapid assessment of the efficacy of novel Wnt inhibitors using zebrafish models. STAR Protoc 2021; 2:100433. [PMID: 33889852 PMCID: PMC8050796 DOI: 10.1016/j.xpro.2021.100433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Dysregulation of Wnt signaling is a hallmark of many cancers, and the development of effective, non-toxic small-molecule Wnt inhibitors is desirable. Off-target toxicities of new compounds are typically tested in mouse models, which is both costly and time consuming. Here, we present a rapid and inexpensive protocol to determine the in vivo toxicity and efficacy of novel Wnt inhibitors in zebrafish using a combination of a fluorescence reporter assay as well as eye rescue and fin regeneration assays. These experiments are completed within 1 week to rapidly narrow drug candidates before moving to more expensive pre-clinical testing. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2020).
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Affiliation(s)
- Meghan G Haney
- University of Kentucky, Department of Molecular and Cellular Biochemistry, Lexington, KY 40509, USA.,University of Kentucky, Markey Cancer Center, Lexington, KY 40509, USA
| | - Mary Wimsett
- University of Kentucky, Department of Molecular and Cellular Biochemistry, Lexington, KY 40509, USA
| | - Chunming Liu
- University of Kentucky, Department of Molecular and Cellular Biochemistry, Lexington, KY 40509, USA.,University of Kentucky, Markey Cancer Center, Lexington, KY 40509, USA
| | - Jessica S Blackburn
- University of Kentucky, Department of Molecular and Cellular Biochemistry, Lexington, KY 40509, USA.,University of Kentucky, Markey Cancer Center, Lexington, KY 40509, USA
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15
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Panuška P, Nejedlá Z, Smejkal J, Aubrecht P, Liegertová M, Štofik M, Havlica J, Malý J. A millifluidic chip for cultivation of fish embryos and toxicity testing fabricated by 3D printing technology. RSC Adv 2021; 11:20507-20518. [PMID: 35479895 PMCID: PMC9033994 DOI: 10.1039/d1ra00846c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/25/2021] [Indexed: 11/21/2022] Open
Abstract
A novel design of 3D printed zebrafish millifluidic system for embryonic long-term cultivation and toxicity screening has been developed. The chip unit provides 24 cultivation chambers and a selective individual embryo removal functionality.
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Affiliation(s)
- Petr Panuška
- Department of Biology
- Faculty of Science
- University of J.E. Purkyne
- 400 96 Usti nad Labem
- Czech Republic
| | - Zuzana Nejedlá
- Department of Biology
- Faculty of Science
- University of J.E. Purkyne
- 400 96 Usti nad Labem
- Czech Republic
| | - Jiří Smejkal
- Department of Biology
- Faculty of Science
- University of J.E. Purkyne
- 400 96 Usti nad Labem
- Czech Republic
| | - Petr Aubrecht
- Department of Biology
- Faculty of Science
- University of J.E. Purkyne
- 400 96 Usti nad Labem
- Czech Republic
| | - Michaela Liegertová
- Department of Biology
- Faculty of Science
- University of J.E. Purkyne
- 400 96 Usti nad Labem
- Czech Republic
| | - Marcel Štofik
- Department of Biology
- Faculty of Science
- University of J.E. Purkyne
- 400 96 Usti nad Labem
- Czech Republic
| | - Jaromír Havlica
- Department of Chemistry
- Faculty of Science
- University of J.E. Purkyne
- 400 96 Usti nad Labem
- Czech Republic
| | - Jan Malý
- Department of Biology
- Faculty of Science
- University of J.E. Purkyne
- 400 96 Usti nad Labem
- Czech Republic
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16
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Colón-Rodríguez A, Uribe-Salazar JM, Weyenberg KB, Sriram A, Quezada A, Kaya G, Jao E, Radke B, Lein PJ, Dennis MY. Assessment of Autism Zebrafish Mutant Models Using a High-Throughput Larval Phenotyping Platform. Front Cell Dev Biol 2020; 8:586296. [PMID: 33330465 PMCID: PMC7719691 DOI: 10.3389/fcell.2020.586296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022] Open
Abstract
In recent years, zebrafish have become commonly used as a model for studying human traits and disorders. Their small size, high fecundity, and rapid development allow for more high-throughput experiments compared to other vertebrate models. Given that zebrafish share >70% gene homologs with humans and their genomes can be readily edited using highly efficient CRISPR methods, we are now able to rapidly generate mutations impacting practically any gene of interest. Unfortunately, our ability to phenotype mutant larvae has not kept pace. To address this challenge, we have developed a protocol that obtains multiple phenotypic measurements from individual zebrafish larvae in an automated and parallel fashion, including morphological features (i.e., body length, eye area, and head size) and movement/behavior. By assaying wild-type zebrafish in a variety of conditions, we determined optimal parameters that avoid significant developmental defects or physical damage; these include morphological imaging of larvae at two time points [3 days post fertilization (dpf) and 5 dpf] coupled with motion tracking of behavior at 5 dpf. As a proof-of-principle, we tested our approach on two novel CRISPR-generated mutant zebrafish lines carrying predicted null-alleles of syngap1b and slc7a5, orthologs to two human genes implicated in autism-spectrum disorder, intellectual disability, and epilepsy. Using our optimized high-throughput phenotyping protocol, we recapitulated previously published results from mouse and zebrafish models of these candidate genes. In summary, we describe a rapid parallel pipeline to characterize morphological and behavioral features of individual larvae in a robust and consistent fashion, thereby improving our ability to better identify genes important in human traits and disorders.
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Affiliation(s)
- Alexandra Colón-Rodríguez
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - José M Uribe-Salazar
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA, United States
| | - KaeChandra B Weyenberg
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Aditya Sriram
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Alejandra Quezada
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.,Sacramento State RISE Program, California State University, Sacramento, Sacramento, CA, United States
| | - Gulhan Kaya
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Emily Jao
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Brittany Radke
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Pamela J Lein
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.,MIND Institute, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Megan Y Dennis
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.,Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA, United States.,MIND Institute, School of Medicine, University of California, Davis, Davis, CA, United States
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17
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Abstract
Metastasis, the dispersal of cancer cells from a primary tumor to secondary sites within the body, is the leading cause of cancer-related death. Animal models have been an indispensable tool to investigate the complex interactions between the cancer cells and the tumor microenvironment during the metastatic cascade. The zebrafish (Danio rerio) has emerged as a powerful vertebrate model for studying metastatic events in vivo. The zebrafish has many attributes including ex-utero development, which facilitates embryonic manipulation, as well as optically transparent tissues, which enables in vivo imaging of fluorescently labeled cells in real time. Here, we summarize the techniques which have been used to study cancer biology and metastasis in the zebrafish model organism, including genetic manipulation and transgenesis, cell transplantation, live imaging, and high-throughput compound screening. Finally, we discuss studies using the zebrafish, which have complemented and benefited metastasis research.
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Affiliation(s)
- Katy R Astell
- The Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
| | - Dirk Sieger
- The Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
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18
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Zhang T, Peterson RT. Modeling Lysosomal Storage Diseases in the Zebrafish. Front Mol Biosci 2020; 7:82. [PMID: 32435656 PMCID: PMC7218095 DOI: 10.3389/fmolb.2020.00082] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/08/2020] [Indexed: 12/13/2022] Open
Abstract
Lysosomal storage diseases (LSDs) are a family of 70 metabolic disorders characterized by mutations in lysosomal proteins that lead to storage material accumulation, multiple-organ pathologies that often involve neurodegeneration, and early mortality in a significant number of patients. Along with the necessity for more effective therapies, there exists an unmet need for further understanding of disease etiology, which could uncover novel pathways and drug targets. Over the past few decades, the growth in knowledge of disease-associated pathways has been facilitated by studies in model organisms, as advancements in mutagenesis techniques markedly improved the efficiency of model generation in mammalian and non-mammalian systems. In this review we highlight non-mammalian models of LSDs, focusing specifically on the zebrafish, a vertebrate model organism that shares remarkable genetic and metabolic similarities with mammals while also conferring unique advantages such as optical transparency and amenability toward high-throughput applications. We examine published zebrafish LSD models and their reported phenotypes, address organism-specific advantages and limitations, and discuss recent technological innovations that could provide potential solutions.
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Affiliation(s)
- T Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, United States
| | - R T Peterson
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, United States
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19
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Gonzales DL, Badhiwala KN, Avants BW, Robinson JT. Bioelectronics for Millimeter-Sized Model Organisms. iScience 2020; 23:100917. [PMID: 32114383 PMCID: PMC7049667 DOI: 10.1016/j.isci.2020.100917] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/29/2020] [Accepted: 02/10/2020] [Indexed: 01/27/2023] Open
Abstract
Advances in microfabrication technologies and biomaterials have enabled a growing class of electronic devices that can stimulate and record bioelectronic signals. Many of these devices have been developed for humans or vertebrate animals, where miniaturization allows for implantation within the body. There are, however, another class of bioelectronic interfaces that exploit microfabrication and nanoelectronics to record signals from tiny, millimeter-sized organisms. In these cases, rather than implanting a device inside an animal, animals themselves are loaded in large numbers into bioelectronic devices for neural circuit and behavioral interrogation. These scalable interfaces provide platforms to develop new therapeutics as well as better understand basic principles of bioelectronic communication, neuroscience, and behavior. Here we review recent progress in these bioelectronic technologies and describe how they can complement on-chip optical, mechanical, and chemical interrogation methods to achieve high-throughput, multimodal studies of millimeter-sized small animals.
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Affiliation(s)
- Daniel L Gonzales
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Dr., West Lafayette, IN 47907, USA
| | - Krishna N Badhiwala
- Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA
| | - Benjamin W Avants
- Department of Electrical and Computer Engineering, Rice University, 6100 Main St., Houston, TX 77005, USA
| | - Jacob T Robinson
- Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA; Department of Electrical and Computer Engineering, Rice University, 6100 Main St., Houston, TX 77005, USA; Applied Physics Program, Rice University, 6100 Main St., Houston, TX 77005, USA; Department of Neuroscience, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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20
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Horowitz LF, Rodriguez AD, Ray T, Folch A. Microfluidics for interrogating live intact tissues. MICROSYSTEMS & NANOENGINEERING 2020; 6:69. [PMID: 32879734 PMCID: PMC7443437 DOI: 10.1038/s41378-020-0164-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 05/08/2023]
Abstract
The intricate microarchitecture of tissues - the "tissue microenvironment" - is a strong determinant of tissue function. Microfluidics offers an invaluable tool to precisely stimulate, manipulate, and analyze the tissue microenvironment in live tissues and engineer mass transport around and into small tissue volumes. Such control is critical in clinical studies, especially where tissue samples are scarce, in analytical sensors, where testing smaller amounts of analytes results in faster, more portable sensors, and in biological experiments, where accurate control of the cellular microenvironment is needed. Microfluidics also provides inexpensive multiplexing strategies to address the pressing need to test large quantities of drugs and reagents on a single biopsy specimen, increasing testing accuracy, relevance, and speed while reducing overall diagnostic cost. Here, we review the use of microfluidics to study the physiology and pathophysiology of intact live tissues at sub-millimeter scales. We categorize uses as either in vitro studies - where a piece of an organism must be excised and introduced into the microfluidic device - or in vivo studies - where whole organisms are small enough to be introduced into microchannels or where a microfluidic device is interfaced with a live tissue surface (e.g. the skin or inside an internal organ or tumor) that forms part of an animal larger than the device. These microfluidic systems promise to deliver functional measurements obtained directly on intact tissue - such as the response of tissue to drugs or the analysis of tissue secretions - that cannot be obtained otherwise.
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Affiliation(s)
- Lisa F. Horowitz
- Department of Bioengineering, University of Washington, Seattle, WA 98195 USA
| | - Adán D. Rodriguez
- Department of Bioengineering, University of Washington, Seattle, WA 98195 USA
| | - Tyler Ray
- Department of Mechanical Engineering, University of Hawaiʻi at Mānoa, Honolulu, HI 96822 USA
| | - Albert Folch
- Department of Bioengineering, University of Washington, Seattle, WA 98195 USA
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21
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Panigrahi B, Chen CY. Microfluidic Transportation Control of Larval Zebrafish through Optomotor Regulations under a Pressure-Driven Flow. MICROMACHINES 2019; 10:mi10120880. [PMID: 31847405 PMCID: PMC6953065 DOI: 10.3390/mi10120880] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 01/19/2023]
Abstract
To perform zebrafish larvae-related experiments within a microfluidic environment, the larvae need to be anesthetized and subsequently transported into respective test sections through mechanical or manual means. However, anesthetization tends to affect larval sensory perceptions, hindering their natural behaviors. Taking into account that juvenile larvae move naturally within their environment by accessing visual as well as hydromechanical cues, this work proposes an experimental framework to transport nonanesthetized larvae within a microfluidic environment by harmonically tuning both of the aforementioned cues. To provide visual cues, computer-animated moving gratings were provided through an in-house-developed control interface that drove the larval optomotor response. In the meantime, to provide hydromechanical cues, the flow rate was tuned using a syringe pump that affected the zebrafish larvae’s lateral line movement. The results obtained (corresponding to different test conditions) suggest that the magnitude of both modalities plays a crucial role in larval transportation and orientation control. For instance, with a flow rate tuning of 0.1 mL/min along with grating parameters of 1 Hz temporal frequency, the average transportation time for larvae that were 5 days postfertilization was recorded at 1.29 ± 0.49 s, which was approximately three times faster than the transportation time required only in the presence of hydromechanical cues.
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22
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Rothenbücher TS, Ledin J, Gibbs D, Engqvist H, Persson C, Hulsart-Billström G. Zebrafish embryo as a replacement model for initial biocompatibility studies of biomaterials and drug delivery systems. Acta Biomater 2019; 100:235-243. [PMID: 31585201 DOI: 10.1016/j.actbio.2019.09.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/02/2019] [Accepted: 09/26/2019] [Indexed: 02/07/2023]
Abstract
The development of new biomaterials and drug delivery systems necessitates animal experimentation to demonstrate biocompatibility and therapeutic efficacy. Reduction and replacement of the requirement to conduct experiment using full-grown animals has been achieved through utilising zebrafish embryos, a promising bridge model between in vitro and in vivo research. In this review, we consider how zebrafish embryos have been utilised to test both the biocompatibility of materials developed to interact with the human body and drug release studies. Furthermore, we outline the advantages and limitations of this model and review legal and ethical issues. We anticipate increasing application of the zebrafish model for biomaterial evaluation in the near future. STATEMENT OF SIGNIFICANCE: This review aims to evaluate the potential application and suitability of the zebrafish model in the development of biomaterials and drug delivery systems. It creates scientific impact and interest because replacement models are desirable to the society and the scientific community. The continuous development of biomaterials calls for the need to provide solutions for biological testing. This review covers the topic of how the FET model can be applied to evaluate biocompatibility. Further, it explores the zebrafish from the wild-type to the mutant form, followed by a discussion about the ethical considerations and concerns when using the FET model.
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23
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White DT, Saxena MT, Mumm JS. Let's get small (and smaller): Combining zebrafish and nanomedicine to advance neuroregenerative therapeutics. Adv Drug Deliv Rev 2019; 148:344-359. [PMID: 30769046 PMCID: PMC6937731 DOI: 10.1016/j.addr.2019.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/21/2018] [Accepted: 01/28/2019] [Indexed: 01/18/2023]
Abstract
Several key attributes of zebrafish make them an ideal model system for the discovery and development of regeneration promoting therapeutics; most notably their robust capacity for self-repair which extends to the central nervous system. Further, by enabling large-scale drug discovery directly in living vertebrate disease models, zebrafish circumvent critical bottlenecks which have driven drug development costs up. This review summarizes currently available zebrafish phenotypic screening platforms, HTS-ready neurodegenerative disease modeling strategies, zebrafish small molecule screens which have succeeded in identifying regeneration promoting compounds and explores how intravital imaging in zebrafish can facilitate comprehensive analysis of nanocarrier biodistribution and pharmacokinetics. Finally, we discuss the benefits and challenges attending the combination of zebrafish and nanoparticle-based drug optimization, highlighting inspiring proof-of-concept studies and looking toward implementation across the drug development community.
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Affiliation(s)
- David T White
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
| | - Meera T Saxena
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA; Luminomics Inc., Baltimore, MD 21286, USA
| | - Jeff S Mumm
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA.
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24
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Jang H, Oakley E, Forbes-Osborne M, Kesler MV, Norcross R, Morris AC, Galperin E. Hematopoietic and neural crest defects in zebrafish shoc2 mutants: a novel vertebrate model for Noonan-like syndrome. Hum Mol Genet 2019; 28:501-514. [PMID: 30329053 DOI: 10.1093/hmg/ddy366] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/12/2018] [Indexed: 12/15/2022] Open
Abstract
The extracellular signal-related kinase 1 and 2 (ERK1/2) pathway is a highly conserved signaling cascade with numerous essential functions in development. The scaffold protein Shoc2 amplifies the activity of the ERK1/2 pathway and is an essential modulator of a variety of signaling inputs. Germline mutations in Shoc2 are associated with the human developmental disease known as the Noonan-like syndrome with loose anagen hair. Clinical manifestations of this disease include congenital heart defects, developmental delays, distinctive facial abnormalities, reduced growth and cognitive deficits along with hair anomalies. The many molecular details of pathogenesis of the Noonan-like syndrome and related developmental disorders, cumulatively called RASopathies, remain poorly understood. Mouse knockouts for Shoc2 are embryonic lethal, emphasizing the need for additional animal models to study the role of Shoc2 in embryonic development. Here, we characterize a zebrafish shoc2 mutant, and show that Shoc2 is essential for development, and that its loss is detrimental for the development of the neural crest and for hematopoiesis. The zebrafish model of the Noonan-like syndrome described here provides a novel system for the study of structure-function analyses and for genetic screens in a tractable vertebrate system.
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Affiliation(s)
- HyeIn Jang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Erin Oakley
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | | | - Melissa V Kesler
- Division of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | - Rebecca Norcross
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Ann C Morris
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Emilia Galperin
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
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25
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A Modular Millifluidic Homeostatic Imaging Plate for Imaging of Larval Zebrafish. Zebrafish 2019; 16:37-46. [DOI: 10.1089/zeb.2018.1684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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26
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Early JJ, Cole KL, Williamson JM, Swire M, Kamadurai H, Muskavitch M, Lyons DA. An automated high-resolution in vivo screen in zebrafish to identify chemical regulators of myelination. eLife 2018; 7:35136. [PMID: 29979149 PMCID: PMC6056238 DOI: 10.7554/elife.35136] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 07/05/2018] [Indexed: 12/23/2022] Open
Abstract
Myelinating oligodendrocytes are essential for central nervous system (CNS) formation and function. Their disruption is implicated in numerous neurodevelopmental, neuropsychiatric and neurodegenerative disorders. However, recent studies have indicated that oligodendrocytes may be tractable for treatment of disease. In recent years, zebrafish have become well established for the study of myelinating oligodendrocyte biology and drug discovery in vivo. Here, by automating the delivery of zebrafish larvae to a spinning disk confocal microscope, we were able to automate high-resolution imaging of myelinating oligodendrocytes in vivo. From there, we developed an image analysis pipeline that facilitated a screen of compounds with epigenetic and post-translational targets for their effects on regulating myelinating oligodendrocyte number. This screen identified novel compounds that strongly promote myelinating oligodendrocyte formation in vivo. Our imaging platform and analysis pipeline is flexible and can be employed for high-resolution imaging-based screens of broad interest using zebrafish.
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Affiliation(s)
- Jason J Early
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,United Kingdom Zebrafish screening facility, University of Edinburgh, Edinburgh, United Kingdom
| | - Katy Lh Cole
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jill M Williamson
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Matthew Swire
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,MRC Centre for Regenerative Medicine, Edinburgh, United Kingdom
| | | | | | - David A Lyons
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,United Kingdom Zebrafish screening facility, University of Edinburgh, Edinburgh, United Kingdom
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27
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Morphometric analysis and neuroanatomical mapping of the zebrafish brain. Methods 2018; 150:49-62. [PMID: 29936090 DOI: 10.1016/j.ymeth.2018.06.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/14/2018] [Indexed: 12/21/2022] Open
Abstract
Large-scale genomic studies have recently identified genetic variants causative for major neurodevelopmental disorders, such as intellectual disability and autism. However, determining how underlying developmental processes are affected by these mutations remains a significant challenge in the field. Zebrafish is an established model system in developmental neurogenetics that may be useful in uncovering the mechanisms of these mutations. Here we describe the use of voxel-intensity, deformation field, and volume-based morphometric techniques for the systematic and unbiased analysis of gene knock-down and environmental exposure-induced phenotypes in zebrafish. We first present a computational method for brain segmentation based on transgene expression patterns to create a comprehensive neuroanatomical map. This map allowed us to disclose statistically significant changes in brain microstructure and composition in neurodevelopmental models. We demonstrate the effectiveness of morphometric techniques in measuring changes in the relative size of neuroanatomical subdivisions in atoh7 morphant larvae and in identifying phenotypes in larvae treated with valproic acid, a chemical demonstrated to increase the risk of autism in humans. These tools enable rigorous evaluation of the effects of gene mutations and environmental exposures on neural development, providing an entry point for cellular and molecular analysis of basic developmental processes as well as neurodevelopmental and neurodegenerative disorders.
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28
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Mani K, Hsieh YC, Panigrahi B, Chen CY. A noninvasive light driven technique integrated microfluidics for zebrafish larvae transportation. BIOMICROFLUIDICS 2018; 12:021101. [PMID: 30867853 PMCID: PMC6404953 DOI: 10.1063/1.5027014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/14/2018] [Indexed: 05/15/2023]
Abstract
Transferring the zebrafish larvae on an imaging platform has long been performed manually by the use of forceps or through mechanical pumping. These methods induce detrimental damages to the fragile bodies of zebrafish larvae during the transportation. To address this issue, in this work we are devising a light driven technique to transport zebrafish larvae within a microfluidic environment. In particular, an optomotor behavioral response of the zebrafish larvae was controlled through the computer animated moving gratings for their transportation within a microfluidics chamber. It was observed that with an optimum grating frequency of 1.5 Hz and a grating width ratio of 1:1, a 5 days-post fertilization zebrafish larva can be transported within minimum and maximum time periods of 0.63 and 2.49 s, respectively. This proposed technique can be utilized towards multi-automatic transportation of zebrafish larvae within the microfluidic environment as well as the zebrafish core facility.
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Affiliation(s)
| | | | | | - Chia-Yuan Chen
- Author to whom correspondence should be addressed: . Telephone: +886-2757575-62169. Fax: +886-2352973
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29
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Bozic I, Li X, Tao Y. Quantitative biometry of zebrafish retinal vasculature using optical coherence tomographic angiography. BIOMEDICAL OPTICS EXPRESS 2018; 9:1244-1255. [PMID: 29541517 PMCID: PMC5846527 DOI: 10.1364/boe.9.001244] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/10/2018] [Accepted: 02/14/2018] [Indexed: 06/01/2023]
Abstract
The zebrafish is a robust model for studying human ophthalmic function and disease because of its fecundity, life-cycle, and similarities between its retinal structure and the human retina. Here, we demonstrate longitudinal in vivo imaging of retinal structure using optical coherence tomography (OCT) and noninvasive retinal vascular perfusion imaging using OCT angiography (OCT-A) in zebrafish. In addition, we present methods for retinal vascular segmentation and biometry to quantify vessel branch length, curvature, and angle. We further motivate retinal vascular biometry as a novel method for noninvasive zebrafish identification and demonstrated 99.9% accuracy for uniquely identifying eyes from a set of 200 longitudinal OCT/OCT-A volumes. The described methods enable the quantitative analysis of the vascular changes in zebrafish models of ophthalmic diseases and may broadly benefit large-scale zebrafish studies.
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Affiliation(s)
- Ivan Bozic
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
- These authors contributed equally in this work
| | - Xiaoyue Li
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
- These authors contributed equally in this work
| | - Yuankai Tao
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
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30
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Liu L, Yang G, Liu S, Wang L, Yang X, Qu H, Liu X, Cao L, Pan W, Li H. High-throughput imaging of zebrafish embryos using a linear-CCD-based flow imaging system. BIOMEDICAL OPTICS EXPRESS 2017; 8:5651-5662. [PMID: 29296494 PMCID: PMC5745109 DOI: 10.1364/boe.8.005651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/28/2017] [Accepted: 11/02/2017] [Indexed: 05/08/2023]
Abstract
High-throughput imaging and screening is essential for biomedical research and drug discovery using miniature model organisms such as zebrafish. This study introduces a high-speed imaging system which illuminates zebrafish embryos flowing through a capillary tube with a sheet of light and captures them using a linear charge-coupled device (CCD). This system can image dozens of zebrafish embryos per second. An image algorithm was developed to recognize each embryo and to perform automatic analysis. We distinguished dead and living embryos according to the gray level distribution and conducted statistics of morphological characteristics of embryos at different growing stages.
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Affiliation(s)
- Lifeng Liu
- School of Electronic Engineering and Optoelectronics Technology, Nanjing University of Science and Technology, Nanjing 210094, China
- Jiangsu Key Laboratory of Medical Optics, CAS Center for Excellence in Molecular Cell Science, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Guang Yang
- Jiangsu Key Laboratory of Medical Optics, CAS Center for Excellence in Molecular Cell Science, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Shoupeng Liu
- Jiangsu Key Laboratory of Medical Optics, CAS Center for Excellence in Molecular Cell Science, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Linbo Wang
- Jiangsu Key Laboratory of Medical Optics, CAS Center for Excellence in Molecular Cell Science, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Xibin Yang
- Jiangsu Key Laboratory of Medical Optics, CAS Center for Excellence in Molecular Cell Science, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Huiming Qu
- School of Electronic Engineering and Optoelectronics Technology, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Xiaofen Liu
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Le Cao
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Weijun Pan
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Hui Li
- Jiangsu Key Laboratory of Medical Optics, CAS Center for Excellence in Molecular Cell Science, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
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31
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Yu Y, Mutlu AS, Liu H, Wang MC. High-throughput screens using photo-highlighting discover BMP signaling in mitochondrial lipid oxidation. Nat Commun 2017; 8:865. [PMID: 29021566 PMCID: PMC5636786 DOI: 10.1038/s41467-017-00944-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 08/04/2017] [Indexed: 01/22/2023] Open
Abstract
High-throughput screens at microscopic resolution can uncover molecular mechanisms of cellular dynamics, but remain technically challenging in live multicellular organisms. Here we present a genetic screening method using photo-highlighting for candidate selection on microscopes. We apply this method to stimulated Raman scattering (SRS) microscopy and systematically identify 57 Caenorhabditis elegans mutants with altered lipid distribution. Four of these mutants target the components of the Bone Morphogenetic Protein (BMP) signaling pathway, revealing that BMP signaling inactivation causes exhaustion of lipid reserves in somatic tissues. Using SRS-based isotope tracing assay to quantitatively track lipid synthesis and mobilization, we discover that the BMP signaling mutants have increased rates of lipid mobilization. Furthermore, this increase is associated with the induction of mitochondrial β-oxidation and mitochondrial fusion. Together these studies demonstrate a photo-highlighting microscopic strategy for genome-scale screens, leading to the discovery of new roles for BMP signaling in linking mitochondrial homeostasis and lipid metabolism.High-throughput genetic screens in animals could benefit from an easy way to mark positive hits. Here the authors introduce photo-highlighting using a photoconvertible fluorescent protein, and in combination with stimulated Raman scattering (SRS) microscopy, define a role for BMP signaling in lipid metabolism in C. elegans.
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Affiliation(s)
- Yong Yu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ayse Sena Mutlu
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Harrison Liu
- Graduate Program in Bioengineering, University of California, San Francisco and University of California, Berkeley, San Francisco, CA, 94143, USA
| | - Meng C Wang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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32
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Gencturk E, Mutlu S, Ulgen KO. Advances in microfluidic devices made from thermoplastics used in cell biology and analyses. BIOMICROFLUIDICS 2017; 11:051502. [PMID: 29152025 PMCID: PMC5654984 DOI: 10.1063/1.4998604] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/11/2017] [Indexed: 05/10/2023]
Abstract
Silicon and glass were the main fabrication materials of microfluidic devices, however, plastics are on the rise in the past few years. Thermoplastic materials have recently been used to fabricate microfluidic platforms to perform experiments on cellular studies or environmental monitoring, with low cost disposable devices. This review describes the present state of the development and applications of microfluidic systems used in cell biology and analyses since the year 2000. Cultivation, separation/isolation, detection and analysis, and reaction studies are extensively discussed, considering only microorganisms (bacteria, yeast, fungi, zebra fish, etc.) and mammalian cell related studies in the microfluidic platforms. The advantages/disadvantages, fabrication methods, dimensions, and the purpose of creating the desired system are explained in detail. An important conclusion of this review is that these microfluidic platforms are still open for research and development, and solutions need to be found for each case separately.
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Affiliation(s)
- Elif Gencturk
- Department of Chemical Engineering, Biosystems Engineering Laboratory, Bogazici University, 34342 Istanbul, Turkey
| | - Senol Mutlu
- Department of Electrical and Electronics Engineering, BUMEMS Laboratory, Bogazici University, 34342 Istanbul, Turkey
| | - Kutlu O Ulgen
- Department of Chemical Engineering, Biosystems Engineering Laboratory, Bogazici University, 34342 Istanbul, Turkey
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33
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Cole KLH, Early JJ, Lyons DA. Drug discovery for remyelination and treatment of MS. Glia 2017; 65:1565-1589. [PMID: 28618073 DOI: 10.1002/glia.23166] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/20/2017] [Accepted: 04/24/2017] [Indexed: 12/19/2022]
Abstract
Glia constitute the majority of the cells in our nervous system, yet there are currently no drugs that target glia for the treatment of disease. Given ongoing discoveries of the many roles of glia in numerous diseases of the nervous system, this is likely to change in years to come. Here we focus on the possibility that targeting the oligodendrocyte lineage to promote regeneration of myelin (remyelination) represents a therapeutic strategy for the treatment of the demyelinating disease multiple sclerosis, MS. We discuss how hypothesis driven studies have identified multiple targets and pathways that can be manipulated to promote remyelination in vivo, and how this work has led to the first ever remyelination clinical trials. We also highlight how recent chemical discovery screens have identified a host of small molecule compounds that promote oligodendrocyte differentiation in vitro. Some of these compounds have also been shown to promote myelin regeneration in vivo, with one already being trialled in humans. Promoting oligodendrocyte differentiation and remyelination represents just one potential strategy for the treatment of MS. The pathology of MS is complex, and its complete amelioration may require targeting multiple biological processes in parallel. Therefore, we present an overview of new technologies and models for phenotypic analyses and screening that can be exploited to study complex cell-cell interactions in in vitro and in vivo systems. Such technological platforms will provide insight into fundamental mechanisms and increase capacities for drug-discovery of relevance to glia and currently intractable disorders of the CNS.
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Affiliation(s)
- Katy L H Cole
- Centre for Neuroregeneration, MS Society Centre for Translational Research, Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - Jason J Early
- Centre for Neuroregeneration, MS Society Centre for Translational Research, Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - David A Lyons
- Centre for Neuroregeneration, MS Society Centre for Translational Research, Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
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34
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Allalou A, Wu Y, Ghannad-Rezaie M, Eimon PM, Yanik MF. Automated deep-phenotyping of the vertebrate brain. eLife 2017; 6:e23379. [PMID: 28406399 PMCID: PMC5441873 DOI: 10.7554/elife.23379] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/07/2017] [Indexed: 11/13/2022] Open
Abstract
Here, we describe an automated platform suitable for large-scale deep-phenotyping of zebrafish mutant lines, which uses optical projection tomography to rapidly image brain-specific gene expression patterns in 3D at cellular resolution. Registration algorithms and correlation analysis are then used to compare 3D expression patterns, to automatically detect all statistically significant alterations in mutants, and to map them onto a brain atlas. Automated deep-phenotyping of a mutation in the master transcriptional regulator fezf2 not only detects all known phenotypes but also uncovers important novel neural deficits that were overlooked in previous studies. In the telencephalon, we show for the first time that fezf2 mutant zebrafish have significant patterning deficits, particularly in glutamatergic populations. Our findings reveal unexpected parallels between fezf2 function in zebrafish and mice, where mutations cause deficits in glutamatergic neurons of the telencephalon-derived neocortex.
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Affiliation(s)
- Amin Allalou
- Massachusetts Institute of Technology, Cambridge, United States
- Uppsala University, Uppsala, Sweden
| | - Yuelong Wu
- Massachusetts Institute of Technology, Cambridge, United States
| | - Mostafa Ghannad-Rezaie
- Massachusetts Institute of Technology, Cambridge, United States
- ETH Zürich, Zürich, Switzerland
| | - Peter M Eimon
- Massachusetts Institute of Technology, Cambridge, United States
| | - Mehmet Fatih Yanik
- Massachusetts Institute of Technology, Cambridge, United States
- ETH Zürich, Zürich, Switzerland
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35
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Meinert T, Gutwein BA, Rohrbach A. Light-sheet microscopy in a glass capillary: feedback holographic control for illumination beam correction. OPTICS LETTERS 2017; 42:350-353. [PMID: 28081110 DOI: 10.1364/ol.42.000350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Light-sheet microscopy enables fast 3D, high-contrast imaging in biology and colloidal sciences. Recently, the controlled transport of living embryos or small colloids through stable glass capillaries is manifold interesting. Although they hardly impair the sample, glass capillaries spoil the image by generating significant aberrations of the illumination and detection light. Here, we analyze the deflection of illuminating Bessel beams at the capillary by k-spectral shifting, and correct for it by a beam deflector. Using cylindrical lenses for astigmatism compensation on the detection side, we demonstrate 3D line-confocal imaging inside a glass capillary over an axial range of ±400 μm.
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Abstract
Skeletal muscle performs an essential function in human physiology with defects in genes encoding a variety of cellular components resulting in various types of inherited muscle disorders. Muscular dystrophies (MDs) are a severe and heterogeneous type of human muscle disease, manifested by progressive muscle wasting and degeneration. The disease pathogenesis and therapeutic options for MDs have been investigated for decades using rodent models, and considerable knowledge has been accumulated on the cause and pathogenetic mechanisms of this group of human disorders. However, due to some differences between disease severity and progression, what is learned in mammalian models does not always transfer to humans, prompting the desire for additional and alternative models. More recently, zebrafish have emerged as a novel and robust animal model for the study of human muscle disease. Zebrafish MD models possess a number of distinct advantages for modeling human muscle disorders, including the availability and ease of generating mutations in homologous disease-causing genes, the ability to image living muscle tissue in an intact animal, and the suitability of zebrafish larvae for large-scale chemical screens. In this chapter, we review the current understanding of molecular and cellular mechanisms involved in MDs, the process of myogenesis in zebrafish, and the structural and functional characteristics of zebrafish larval muscles. We further discuss the insights gained from the key zebrafish MD models that have been so far generated, and we summarize the attempts that have been made to screen for small molecules inhibitors of the dystrophic phenotypes using these models. Overall, these studies demonstrate that zebrafish is a useful in vivo system for modeling aspects of human skeletal muscle disorders. Studies using these models have contributed both to the understanding of the pathogenesis of muscle wasting disorders and demonstrated their utility as highly relevant models to implement therapeutic screening regimens.
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Affiliation(s)
- M Li
- Monash University, Clayton, VIC, Australia
| | - K J Hromowyk
- The Ohio State University, Columbus, OH, United States
| | - S L Amacher
- The Ohio State University, Columbus, OH, United States
| | - P D Currie
- Monash University, Clayton, VIC, Australia
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Podechard N, Chevanne M, Fernier M, Tête A, Collin A, Cassio D, Kah O, Lagadic-Gossmann D, Sergent O. Zebrafish larva as a reliable model for in vivo assessment of membrane remodeling involvement in the hepatotoxicity of chemical agents. J Appl Toxicol 2016; 37:732-746. [PMID: 27896850 DOI: 10.1002/jat.3421] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/20/2016] [Accepted: 10/28/2016] [Indexed: 12/13/2022]
Abstract
The easy-to-use in vivo model, zebrafish larva, is being increasingly used to screen chemical-induced hepatotoxicity, with a good predictivity for various mechanisms of liver injury. However, nothing is known about its applicability in exploring the mechanism called membrane remodeling, depicted as changes in membrane fluidity or lipid raft properties. The aim of this study was, therefore, to substantiate the zebrafish larva as a suitable in vivo model in this context. Ethanol was chosen as a prototype toxicant because it is largely described, both in hepatocyte cultures and in rodents, as capable of inducing a membrane remodeling leading to hepatocyte death and liver injury. The zebrafish larva model was demonstrated to be fully relevant as membrane remodeling was maintained even after a 1-week exposure without any adaptation as usually reported in rodents and hepatocyte cultures. It was also proven to exhibit a high sensitivity as it discriminated various levels of cytotoxicity depending on the extent of changes in membrane remodeling. In this context, its sensitivity appeared higher than that of WIF-B9 hepatic cells, which is suited for analyzing this kind of hepatotoxicity. Finally, the protection afforded by a membrane stabilizer, ursodeoxycholic acid (UDCA), or by a lipid raft disrupter, pravastatin, definitely validated zebrafish larva as a reliable model to quickly assess membrane remodeling involvement in chemical-induced hepatotoxicity. In conclusion, this model, compatible with a high throughput screening, might be adapted to seek hepatotoxicants via membrane remodeling, and also drugs targeting membrane features to propose new preventive or therapeutic strategies in chemical-induced liver diseases. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Normand Podechard
- UMR Inserm 1085, IRSET, UFR des Sciences Pharmaceutiques et Biologiques, bâtiment 5, 35043, Rennes Cédex, France.,Biosit UMS3480, Université de Rennes 1, 35043, Rennes Cédex, France
| | - Martine Chevanne
- UMR Inserm 1085, IRSET, UFR des Sciences Pharmaceutiques et Biologiques, bâtiment 5, 35043, Rennes Cédex, France.,Biosit UMS3480, Université de Rennes 1, 35043, Rennes Cédex, France
| | - Morgane Fernier
- UMR Inserm 1085, IRSET, UFR des Sciences Pharmaceutiques et Biologiques, bâtiment 5, 35043, Rennes Cédex, France.,Biosit UMS3480, Université de Rennes 1, 35043, Rennes Cédex, France
| | - Arnaud Tête
- UMR Inserm 1085, IRSET, UFR des Sciences Pharmaceutiques et Biologiques, bâtiment 5, 35043, Rennes Cédex, France.,Biosit UMS3480, Université de Rennes 1, 35043, Rennes Cédex, France
| | - Aurore Collin
- UMR Inserm 1085, IRSET, UFR des Sciences Pharmaceutiques et Biologiques, bâtiment 5, 35043, Rennes Cédex, France.,Biosit UMS3480, Université de Rennes 1, 35043, Rennes Cédex, France
| | - Doris Cassio
- Inserm, UMR-S 757; Orsay, France; Université Paris-Sud, Orsay, France
| | - Olivier Kah
- Biosit UMS3480, Université de Rennes 1, 35043, Rennes Cédex, France.,UMR Inserm 1085, IRSET, Université de Rennes 1, bâtiment 9, 35000, Rennes, France
| | - Dominique Lagadic-Gossmann
- UMR Inserm 1085, IRSET, UFR des Sciences Pharmaceutiques et Biologiques, bâtiment 5, 35043, Rennes Cédex, France.,Biosit UMS3480, Université de Rennes 1, 35043, Rennes Cédex, France
| | - Odile Sergent
- UMR Inserm 1085, IRSET, UFR des Sciences Pharmaceutiques et Biologiques, bâtiment 5, 35043, Rennes Cédex, France.,Biosit UMS3480, Université de Rennes 1, 35043, Rennes Cédex, France
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38
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Mani K, Chang Chien TC, Panigrahi B, Chen CY. Manipulation of zebrafish's orientation using artificial cilia in a microchannel with actively adaptive wall design. Sci Rep 2016; 6:36385. [PMID: 27821862 PMCID: PMC5099576 DOI: 10.1038/srep36385] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/12/2016] [Indexed: 12/15/2022] Open
Abstract
The zebrafish is a powerful genetic model organism especially in the biomedical chapter for new drug discovery and development. The genetic toolbox which this vertebrate possesses opens a new window to investigate the etiology of human diseases with a high degree genetic similarity. Still, the requirements of laborious and time-consuming of contemporary zebrafish processing assays limit the procedure in carrying out such genetic screen at high throughput. Here, a zebrafish control scheme was initiated which includes the design and validation of a microfluidic platform to significantly increase the throughput and performance of zebrafish larvae manipulation using the concept of artificial cilia actuation. A moving wall design was integrated into this microfluidic platform first time in literature to accommodate zebrafish inside the microchannel from 1 day post-fertilization (dpf) to 6 dpf and can be further extended to 9 dpf for axial orientation control in a rotational range between 0 to 25 degrees at the minimum step of 2-degree increment in a stepwise manner. This moving wall feature was performed through the deflection of shape memory alloy wire embedded inside the microchannel controlled by the electrical waveforms with high accuracy.
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Affiliation(s)
- Karthick Mani
- Department of Mechanical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Tsung-Chun Chang Chien
- Department of Mechanical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Bivas Panigrahi
- Department of Mechanical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Chia-Yuan Chen
- Department of Mechanical Engineering, National Cheng Kung University, Tainan 701, Taiwan
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Liu H, Chen S, Huang K, Kim J, Mo H, Iovine R, Gendre J, Pascal P, Li Q, Sun Y, Dong Z, Arkin M, Guo S, Huang B. A High-Content Larval Zebrafish Brain Imaging Method for Small Molecule Drug Discovery. PLoS One 2016; 11:e0164645. [PMID: 27732643 PMCID: PMC5061318 DOI: 10.1371/journal.pone.0164645] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/28/2016] [Indexed: 01/01/2023] Open
Abstract
Drug discovery in whole-organisms such as zebrafish is a promising approach for identifying biologically-relevant lead compounds. However, high content imaging of zebrafish at cellular resolution is challenging due to the difficulty in orienting larvae en masse such that the cell type of interest is in clear view. We report the development of the multi-pose imaging method, which uses 96-well round bottom plates combined with a standard liquid handler to repose the larvae within each well multiple times, such that an image in a specific orientation can be acquired. We have validated this method in a chemo-genetic zebrafish model of dopaminergic neuron degeneration. For this purpose, we have developed an analysis pipeline that identifies the larval brain in each image and then quantifies neuronal health in CellProfiler. Our method achieves a SSMD* score of 6.96 (robust Z’-factor of 0.56) and is suitable for screening libraries up to 105 compounds in size.
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Affiliation(s)
- Harrison Liu
- Joint Graduate Program in Bioengineering, University of California, San Francisco and University of California, Berkeley, California, United States of America
| | - Steven Chen
- Small Molecule Discovery Center, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Kevin Huang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Jeffrey Kim
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Han Mo
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Raffael Iovine
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Julie Gendre
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Pauline Pascal
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Qiang Li
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Yaping Sun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Zhiqiang Dong
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Michelle Arkin
- Small Molecule Discovery Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Su Guo
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (SG); (BH)
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (SG); (BH)
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40
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Abstract
Zebrafish ( Danio rerio) is an important vertebrate model organism in biomedical research, especially suitable for morphological screening due to its transparent body during early development. Deep learning has emerged as a dominant paradigm for data analysis and found a number of applications in computer vision and image analysis. Here we demonstrate the potential of a deep learning approach for accurate high-throughput classification of whole-body zebrafish deformations in multifish microwell plates. Deep learning uses the raw image data as an input, without the need of expert knowledge for feature design or optimization of the segmentation parameters. We trained the deep learning classifier on as few as 84 images (before data augmentation) and achieved a classification accuracy of 92.8% on an unseen test data set that is comparable to the previous state of the art (95%) based on user-specified segmentation and deformation metrics. Ablation studies by digitally removing whole fish or parts of the fish from the images revealed that the classifier learned discriminative features from the image foreground, and we observed that the deformations of the head region, rather than the visually apparent bent tail, were more important for good classification performance.
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Affiliation(s)
- Omer Ishaq
- 1 Centre for Image Analysis/SciLifeLab, Uppsala University, Uppsala, Sweden
| | | | - Carolina Wählby
- 1 Centre for Image Analysis/SciLifeLab, Uppsala University, Uppsala, Sweden
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41
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Abstract
Phenotypic drug discovery (PDD) strategies are defined by screening and selection of hit or lead compounds based on quantifiable phenotypic endpoints without prior knowledge of the drug target. We outline the challenges associated with traditional phenotypic screening strategies and propose solutions and new opportunities to be gained by adopting modern PDD technologies. We highlight both historical and recent examples of approved drugs and new drug candidates discovered by modern phenotypic screening. Finally, we offer a prospective view of a new era of PDD underpinned by a wealth of technology advances in the areas of in vitro model development, high-content imaging and image informatics, mechanism-of-action profiling and target deconvolution.
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42
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Planchart A, Mattingly CJ, Allen D, Ceger P, Casey W, Hinton D, Kanungo J, Kullman SW, Tal T, Bondesson M, Burgess SM, Sullivan C, Kim C, Behl M, Padilla S, Reif DM, Tanguay RL, Hamm J. Advancing toxicology research using in vivo high throughput toxicology with small fish models. ALTEX 2016; 33:435-452. [PMID: 27328013 PMCID: PMC5270630 DOI: 10.14573/altex.1601281] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/31/2016] [Indexed: 12/18/2022]
Abstract
Small freshwater fish models, especially zebrafish, offer advantages over traditional rodent models, including low maintenance and husbandry costs, high fecundity, genetic diversity, physiology similar to that of traditional biomedical models, and reduced animal welfare concerns. The Collaborative Workshop on Aquatic Models and 21st Century Toxicology was held at North Carolina State University on May 5-6, 2014, in Raleigh, North Carolina, USA. Participants discussed the ways in which small fish are being used as models to screen toxicants and understand mechanisms of toxicity. Workshop participants agreed that the lack of standardized protocols is an impediment to broader acceptance of these models, whereas development of standardized protocols, validation, and subsequent regulatory acceptance would facilitate greater usage. Given the advantages and increasing application of small fish models, there was widespread interest in follow-up workshops to review and discuss developments in their use. In this article, we summarize the recommendations formulated by workshop participants to enhance the utility of small fish species in toxicology studies, as well as many of the advances in the field of toxicology that resulted from using small fish species, including advances in developmental toxicology, cardiovascular toxicology, neurotoxicology, and immunotoxicology. We alsoreview many emerging issues that will benefit from using small fish species, especially zebrafish, and new technologies that will enable using these organisms to yield results unprecedented in their information content to better understand how toxicants affect development and health.
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Affiliation(s)
- Antonio Planchart
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Carolyn J. Mattingly
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - David Allen
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
| | - Patricia Ceger
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
| | - Warren Casey
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - David Hinton
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Jyotshna Kanungo
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Seth W. Kullman
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Tamara Tal
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Maria Bondesson
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX, USA
| | | | - Con Sullivan
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, USA
| | - Carol Kim
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, USA
| | - Mamta Behl
- Division of National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Stephanie Padilla
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - David M. Reif
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Robert L. Tanguay
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Jon Hamm
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
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43
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Yalikun Y, Tanaka Y. Large-Scale Integration of All-Glass Valves on a Microfluidic Device. MICROMACHINES 2016; 7:mi7050083. [PMID: 30404259 PMCID: PMC6190260 DOI: 10.3390/mi7050083] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 11/17/2022]
Abstract
In this study, we developed a method for fabricating a microfluidic device with integrated large-scale all-glass valves and constructed an actuator system to control each of the valves on the device. Such a microfluidic device has advantages that allow its use in various fields, including physical, chemical, and biochemical analyses and syntheses. However, it is inefficient and difficult to integrate the large-scale all-glass valves in a microfluidic device using conventional glass fabrication methods, especially for the through-hole fabrication step. Therefore, we have developed a fabrication method for the large-scale integration of all-glass valves in a microfluidic device that contains 110 individually controllable diaphragm valve units on a 30 mm × 70 mm glass slide. This prototype device was fabricated by first sandwiching a 0.4-mm-thick glass slide that contained 110 1.5-mm-diameter shallow chambers, each with two 50-μm-diameter through-holes, between an ultra-thin glass sheet (4 μm thick) and another 0.7-mm-thick glass slide that contained etched channels. After the fusion bonding of these three layers, the large-scale microfluidic device was obtained with integrated all-glass valves consisting of 110 individual diaphragm valve units. We demonstrated its use as a pump capable of generating a flow rate of approximately 0.06–5.33 μL/min. The maximum frequency of flow switching was approximately 12 Hz.
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Affiliation(s)
- Yaxiaer Yalikun
- Laboratory for Integrated Biodevice Unit, Quantitative Biology Center, RIKEN, Suita, Osaka 565-0871, Japan.
| | - Yo Tanaka
- Laboratory for Integrated Biodevice Unit, Quantitative Biology Center, RIKEN, Suita, Osaka 565-0871, Japan.
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Yang F, Gao C, Wang P, Zhang GJ, Chen Z. Fish-on-a-chip: microfluidics for zebrafish research. LAB ON A CHIP 2016; 16:1106-25. [PMID: 26923141 DOI: 10.1039/c6lc00044d] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
High-efficiency zebrafish (embryo) handling platforms are crucially needed to facilitate the deciphering of the increasingly expanding vertebrate-organism model values. However, the manipulation platforms for zebrafish are scarce and rely mainly on the conventional "static" microtiter plates or glass slides with rigid gel, which limits the dynamic, three-dimensional (3D), tissue/organ-oriented information acquisition from the intact larva with normal developmental dynamics. In addition, these routine platforms are not amenable to high-throughput handling of such swimming multicellular biological entities at the single-organism level and incapable of precisely controlling the growth microenvironment by delivering stimuli in a well-defined spatiotemporal fashion. Recently, microfluidics has been developed to address these technical challenges via tailor-engineered microscale structures or structured arrays, which integrate with or interface to functional components (e.g. imaging systems), allowing quantitative readouts of small objects (zebrafish larvae and embryos) under normal physiological conditions. Here, we critically review the recent progress on zebrafish manipulation, imaging and phenotype readouts of external stimuli using these microfluidic tools and discuss the challenges that confront these promising "fish-on-a-chip" technologies. We also provide an outlook on future potential trends in this field by combining with bionanoprobes and biosensors.
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Affiliation(s)
- Fan Yang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China.
| | - Chuan Gao
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China.
| | - Ping Wang
- School of Basic Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China.
| | - Zuanguang Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
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Pulak R. Tools for automating the imaging of zebrafish larvae. Methods 2016; 96:118-126. [DOI: 10.1016/j.ymeth.2015.11.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022] Open
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Cunliffe VT. Building a zebrafish toolkit for investigating the pathobiology of epilepsy and identifying new treatments for epileptic seizures. J Neurosci Methods 2016. [DOI: 10.1016/j.jneumeth.2015.07.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Ardeshiri R, Hosseini L, Amini N, Rezai P. Cardiac screening of intact Drosophila melanogaster larvae under exposure to aqueous and gaseous toxins in a microfluidic device. RSC Adv 2016. [DOI: 10.1039/c6ra14159e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We present a semi-automated microfluidic chip for orientation, immobilization, chemical exposure, and cardiac screening of 3rd instar Drosophila melanogaster larvae.
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Affiliation(s)
- R. Ardeshiri
- Department of Mechanical Engineering
- York University
- Toronto
- Canada
| | - L. Hosseini
- Department of Mechanical Engineering
- York University
- Toronto
- Canada
| | - N. Amini
- Department of Mechanical Engineering
- York University
- Toronto
- Canada
| | - P. Rezai
- Department of Mechanical Engineering
- York University
- Toronto
- Canada
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Guan Z, Lee J, Jiang H, Dong S, Jen N, Hsiai T, Ho CM, Fei P. Compact plane illumination plugin device to enable light sheet fluorescence imaging of multi-cellular organisms on an inverted wide-field microscope. BIOMEDICAL OPTICS EXPRESS 2016; 7:194-208. [PMID: 26819828 PMCID: PMC4722903 DOI: 10.1364/boe.7.000194] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/06/2015] [Accepted: 12/08/2015] [Indexed: 05/05/2023]
Abstract
We developed a compact plane illumination plugin (PIP) device which enabled plane illumination and light sheet fluorescence imaging on a conventional inverted microscope. The PIP device allowed the integration of microscope with tunable laser sheet profile, fast image acquisition, and 3-D scanning. The device is both compact, measuring approximately 15 by 5 by 5 cm, and cost-effective, since we employed consumer electronics and an inexpensive device molding method. We demonstrated that PIP provided significant contrast and resolution enhancement to conventional microscopy through imaging different multi-cellular fluorescent structures, including 3-D branched cells in vitro and live zebrafish embryos. Imaging with the integration of PIP greatly reduced out-of-focus contamination and generated sharper contrast in acquired 2-D plane images when compared with the stand-alone inverted microscope. As a result, the dynamic fluid domain of the beating zebrafish heart was clearly segmented and the functional monitoring of the heart was achieved. Furthermore, the enhanced axial resolution established by thin plane illumination of PIP enabled the 3-D reconstruction of the branched cellular structures, which leads to the improvement on the functionality of the wide field microscopy.
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Affiliation(s)
- Zeyi Guan
- Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, 90095, USA
- contributed equally
| | - Juhyun Lee
- Biomedical Engineering, University of California, Los Angeles, Los Angeles, 90095, USA
- contributed equally
| | - Hao Jiang
- School of Mechanical and Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Siyan Dong
- Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, 90095, USA
| | - Nelson Jen
- Biomedical Engineering, University of California, Los Angeles, Los Angeles, 90095, USA
| | - Tzung Hsiai
- Biomedical Engineering, University of California, Los Angeles, Los Angeles, 90095, USA
- School of Medicine, University of California, Los Angeles, Los Angeles, 90095, USA
| | - Chih-Ming Ho
- Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, 90095, USA
| | - Peng Fei
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, 430074, China
- Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, 90095, USA
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Abstract
Zebrafish embryos can be obtained for research purposes in large numbers at low cost and embryos develop externally in limited space, making them highly suitable for high-throughput cancer studies and drug screens. Non-invasive live imaging of various processes within the larvae is possible due to their transparency during development, and a multitude of available fluorescent transgenic reporter lines.To perform high-throughput studies, handling large amounts of embryos and larvae is required. With such high number of individuals, even minute tasks may become time-consuming and arduous. In this chapter, an overview is given of the developments in the automation of various steps of large scale zebrafish cancer research for discovering important cancer pathways and drugs for the treatment of human disease. The focus lies on various tools developed for cancer cell implantation, embryo handling and sorting, microfluidic systems for imaging and drug treatment, and image acquisition and analysis. Examples will be given of employment of these technologies within the fields of toxicology research and cancer research.
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Dang M, Fogley R, Zon LI. Identifying Novel Cancer Therapies Using Chemical Genetics and Zebrafish. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:103-24. [PMID: 27165351 DOI: 10.1007/978-3-319-30654-4_5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemical genetics is the use of small molecules to perturb biological pathways. This technique is a powerful tool for implicating genes and pathways in developmental programs and disease, and simultaneously provides a platform for the discovery of novel therapeutics. The zebrafish is an advantageous model for in vivo high-throughput small molecule screening due to translational appeal, high fecundity, and a unique set of developmental characteristics that support genetic manipulation, chemical treatment, and phenotype detection. Chemical genetic screens in zebrafish can identify hit compounds that target oncogenic processes-including cancer initiation and maintenance, metastasis, and angiogenesis-and may serve as cancer therapies. Notably, by combining drug discovery and animal testing, in vivo screening of small molecules in zebrafish has enabled rapid translation of hit anti-cancer compounds to the clinic, especially through the repurposing of FDA-approved drugs. Future technological advancements in automation and high-powered imaging, as well as the development and characterization of new mutant and transgenic lines, will expand the scope of chemical genetics in zebrafish.
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Affiliation(s)
- Michelle Dang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA.,Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, 1 Blackfan Circle, Boston, MA, 02115, USA
| | - Rachel Fogley
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA.,Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, 1 Blackfan Circle, Boston, MA, 02115, USA
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA. .,Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, 1 Blackfan Circle, Boston, MA, 02115, USA.
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