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Linsley JW, Reisine T, Finkbeiner S. Three dimensional (3D) and four dimensional (4D) live imaging to study mechanisms of progressive neurodegeneration. J Biol Chem 2024:107433. [PMID: 38825007 DOI: 10.1016/j.jbc.2024.107433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 05/20/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024] Open
Abstract
Neurodegenerative diseases are complex and progressive, posing challenges to their study and understanding. Recent advances in microscopy imaging technologies have enabled the exploration of neurons in three spatial dimensions (3D) over time (4D). When applied to 3D cultures, tissues or animals, these technologies can provide valuable insights into the dynamic and spatial nature of neurodegenerative diseases. This review focuses on the use of imaging techniques and neurodegenerative disease models to study neurodegeneration in 4D. Imaging techniques such as confocal microscopy, two-photon microscopy, miniscope imaging, light sheet microscopy, and robotic microscopy offer powerful tools to visualize and analyze neuronal changes over time in 3D tissue. Application of these technologies to in vitro models of neurodegeneration such as mouse organotypic culture systems and human organoid models provide versatile platforms to study neurodegeneration in a physiologically relevant context. Additionally, use of 4D imaging in vivo, including in mouse and zebrafish models of neurodegenerative diseases, allows for the investigation of early dysfunction and behavioral changes associated with neurodegeneration. We propose that these studies have the power to overcome the limitations of two-dimensional (2D) monolayer neuronal cultures, and pave the way for improved understanding of the dynamics of neurodegenerative diseases and the development of effective therapeutic strategies.
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Affiliation(s)
- Jeremy W Linsley
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA; Operant Biopharma, San Francisco, CA 94158, USA
| | - Terry Reisine
- Independent scientific consultant, Santa Cruz CA, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA; Operant Biopharma, San Francisco, CA 94158, USA; Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, San Francisco, CA 94158, USA; Departments of Neurology and Physiology, University of California, San Francisco, CA 94158, USA; Neuroscience Graduate Program, University of California, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA
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Linsley JW, Linsley DA, Lamstein J, Ryan G, Shah K, Castello NA, Oza V, Kalra J, Wang S, Tokuno Z, Javaherian A, Serre T, Finkbeiner S. Superhuman cell death detection with biomarker-optimized neural networks. SCIENCE ADVANCES 2021; 7:eabf8142. [PMID: 34878844 PMCID: PMC8654296 DOI: 10.1126/sciadv.abf8142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 10/19/2021] [Indexed: 05/02/2023]
Abstract
Cellular events underlying neurodegenerative disease may be captured by longitudinal live microscopy of neurons. While the advent of robot-assisted microscopy has helped scale such efforts to high-throughput regimes with the statistical power to detect transient events, time-intensive human annotation is required. We addressed this fundamental limitation with biomarker-optimized convolutional neural networks (BO-CNNs): interpretable computer vision models trained directly on biosensor activity. We demonstrate the ability of BO-CNNs to detect cell death, which is typically measured by trained annotators. BO-CNNs detected cell death with superhuman accuracy and speed by learning to identify subcellular morphology associated with cell vitality, despite receiving no explicit supervision to rely on these features. These models also revealed an intranuclear morphology signal that is difficult to spot by eye and had not previously been linked to cell death, but that reliably indicates death. BO-CNNs are broadly useful for analyzing live microscopy and essential for interpreting high-throughput experiments.
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Affiliation(s)
- Jeremy W. Linsley
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Drew A. Linsley
- Robert J. & Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
- Department of Cognitive, Linguistic & Psychological Sciences, Brown University, Providence, RI 02912, USA
| | - Josh Lamstein
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Gennadi Ryan
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Kevan Shah
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Nicholas A. Castello
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Viral Oza
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jaslin Kalra
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Shijie Wang
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Zachary Tokuno
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ashkan Javaherian
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Thomas Serre
- Robert J. & Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
- Department of Cognitive, Linguistic & Psychological Sciences, Brown University, Providence, RI 02912, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA
- Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, San Francisco, CA 94158, USA
- Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
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Finkbeiner S. Functional genomics, genetic risk profiling and cell phenotypes in neurodegenerative disease. Neurobiol Dis 2020; 146:105088. [PMID: 32977020 PMCID: PMC7686089 DOI: 10.1016/j.nbd.2020.105088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 09/11/2020] [Accepted: 09/18/2020] [Indexed: 12/03/2022] Open
Abstract
Human genetics provides unbiased insights into the causes of human disease, which can be used to create a foundation for effective ways to more accurately diagnose patients, stratify patients for more successful clinical trials, discover and develop new therapies, and ultimately help patients choose the safest and most promising therapeutic option based on their risk profile. But the process for translating basic observations from human genetics studies into pathogenic disease mechanisms and treatments is laborious and complex, and this challenge has particularly slowed the development of interventions for neurodegenerative disease. In this review, we discuss the many steps in the process, the important considerations at each stage, and some of the latest tools and technologies that are available to help investigators translate insights from human genetics into diagnostic and therapeutic strategies that will lead to the sort of advances in clinical care that make a difference for patients.
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Affiliation(s)
- Steven Finkbeiner
- Center for Systems and Therapeutics, USA; Taube/Koret Center for Neurodegenerative Disease Research, Gladstone Institutes, San Francisco, CA 94158, USA; Departments of Neurology and Physiology, University of Califorina, San Francisco, CA 94158, USA.
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Linsley JW, Reisine T, Finkbeiner S. Cell death assays for neurodegenerative disease drug discovery. Expert Opin Drug Discov 2019; 14:901-913. [PMID: 31179783 DOI: 10.1080/17460441.2019.1623784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction: Neurodegenerative diseases affect millions of people worldwide. Neurodegeneration is gradual over time, characterized by neuronal death that causes deterioration of cognitive or motor functions, ultimately leading to the patient's death. Currently, there are no treatments that effectively slow the progression of any neurodegenerative disease, but improved microscopy assays and models for neurodegeneration could lead the way to the discovery of disease-modifying therapeutics. Areas covered: Herein, the authors describe cell-based assays used to discover drugs with the potential to slow neurodegeneration, and their associated disease models. They focus on microscopy technologies that can be adapted to a high-throughput screening format that both detect cell death and monitor early signs of neurodegeneration and functional changes to identify drugs that the block early stages of neurodegeneration. Expert opinion: Many different phenotypes have been used in screens for the development of therapeutics towards neurodegenerative disease. The context of each phenotype in relation to neurodegeneration must be established to identify therapeutics likely to successfully target and treat disease. The use of improved models of neurodegeneration, statistical analyses, computational models, and improved markers of neuronal death will help in this pursuit and lead to better screening methods to identify therapeutic compounds against neurodegenerative disease.
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Affiliation(s)
- Jeremy W Linsley
- a Gladstone Center for Systems and Therapeutics , San Francisco , CA , USA
| | - Terry Reisine
- b Independent scientific consultant , Santa Cruz , CA , USA
| | - Steven Finkbeiner
- a Gladstone Center for Systems and Therapeutics , San Francisco , CA , USA.,c Neuroscience Graduate Program, University of California , San Francisco , CA , USA.,d Biomedical Sciences and Neuroscience Graduate Program, University of California , San Francisco , CA , USA.,e Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes , San Francisco , CA , USA.,f Department of Neurology, University of California , San Francisco , CA , USA.,g Department of Physiology, University of California , San Francisco , CA , USA
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Linsley JW, Tripathi A, Epstein I, Schmunk G, Mount E, Campioni M, Oza V, Barch M, Javaherian A, Nowakowski TJ, Samsi S, Finkbeiner S. Automated four-dimensional long term imaging enables single cell tracking within organotypic brain slices to study neurodevelopment and degeneration. Commun Biol 2019; 2:155. [PMID: 31069265 PMCID: PMC6494885 DOI: 10.1038/s42003-019-0411-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/18/2019] [Indexed: 02/08/2023] Open
Abstract
Current approaches for dynamic profiling of single cells rely on dissociated cultures, which lack important biological features existing in tissues. Organotypic slice cultures preserve aspects of structural and synaptic organisation within the brain and are amenable to microscopy, but established techniques are not well adapted for high throughput or longitudinal single cell analysis. Here we developed a custom-built, automated confocal imaging platform, with improved organotypic slice culture and maintenance. The approach enables fully automated image acquisition and four-dimensional tracking of morphological changes within individual cells in organotypic cultures from rodent and human primary tissues for at least 3 weeks. To validate this system, we analysed neurons expressing a disease-associated version of huntingtin (HTT586Q138-EGFP), and observed that they displayed hallmarks of Huntington's disease and died sooner than controls. By facilitating longitudinal single-cell analyses of neuronal physiology, our system bridges scales necessary to attain statistical power to detect developmental and disease phenotypes.
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Affiliation(s)
- Jeremy W Linsley
- Gladstone Center for Systems and Therapeutics, San Francisco, CA 94158 USA
| | - Atmiyata Tripathi
- Gladstone Center for Systems and Therapeutics, San Francisco, CA 94158 USA
| | - Irina Epstein
- Gladstone Center for Systems and Therapeutics, San Francisco, CA 94158 USA
| | - Galina Schmunk
- 2Department of Anatomy, University of California, San Francisco, CA 94158 USA
| | - Elliot Mount
- Gladstone Center for Systems and Therapeutics, San Francisco, CA 94158 USA
| | - Matthew Campioni
- Gladstone Center for Systems and Therapeutics, San Francisco, CA 94158 USA
| | - Viral Oza
- Gladstone Center for Systems and Therapeutics, San Francisco, CA 94158 USA
| | - Mariya Barch
- Gladstone Center for Systems and Therapeutics, San Francisco, CA 94158 USA
| | - Ashkan Javaherian
- Gladstone Center for Systems and Therapeutics, San Francisco, CA 94158 USA
| | - Tomasz J Nowakowski
- 2Department of Anatomy, University of California, San Francisco, CA 94158 USA
| | - Siddharth Samsi
- 3Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, L-4367 Luxembourg
- 9Present Address: MIT Lincoln Laboratory, Lexington, MA 02421 USA
| | - Steven Finkbeiner
- Gladstone Center for Systems and Therapeutics, San Francisco, CA 94158 USA
- 4Neuroscience Graduate Program, University of California, San Francisco, CA 94158 USA
- 5Biomedical Sciences and Neuroscience Graduate Program, University of California, San Francisco, CA 94143 USA
- 6Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, San Francisco, CA 94158 USA
- 7Department of Neurology, University of California, San Francisco, CA 94158 USA
- 8Department of Physiology, University of California, San Francisco, CA 94158 USA
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Allen J. Robotic Microscopy with the Nikon Ti2 for high-content analysis applications. Nat Methods 2016. [DOI: 10.1038/nmeth.f.400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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