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Hoffmann C, Cho E, Zalesky A, Di Biase MA. From pixels to connections: exploring in vitro neuron reconstruction software for network graph generation. Commun Biol 2024; 7:571. [PMID: 38750282 PMCID: PMC11096190 DOI: 10.1038/s42003-024-06264-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
Digital reconstruction has been instrumental in deciphering how in vitro neuron architecture shapes information flow. Emerging approaches reconstruct neural systems as networks with the aim of understanding their organization through graph theory. Computational tools dedicated to this objective build models of nodes and edges based on key cellular features such as somata, axons, and dendrites. Fully automatic implementations of these tools are readily available, but they may also be purpose-built from specialized algorithms in the form of multi-step pipelines. Here we review software tools informing the construction of network models, spanning from noise reduction and segmentation to full network reconstruction. The scope and core specifications of each tool are explicitly defined to assist bench scientists in selecting the most suitable option for their microscopy dataset. Existing tools provide a foundation for complete network reconstruction, however more progress is needed in establishing morphological bases for directed/weighted connectivity and in software validation.
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Affiliation(s)
- Cassandra Hoffmann
- Systems Neuroscience Lab, Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Parkville, Australia.
| | - Ellie Cho
- Biological Optical Microscopy Platform, University of Melbourne, Parkville, Australia
| | - Andrew Zalesky
- Systems Neuroscience Lab, Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Parkville, Australia
- Department of Biomedical Engineering, The University of Melbourne, Parkville, Australia
| | - Maria A Di Biase
- Systems Neuroscience Lab, Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Parkville, Australia
- Stem Cell Disease Modelling Lab, Department of Anatomy and Physiology, The University of Melbourne, Parkville, Australia
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
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Eichholz K, Li AZ, Diem K, Jensen MC, Zhu J, Corey L. A CAR RNA FISH assay to study functional and spatial heterogeneity of chimeric antigen receptor T cells in tissue. Sci Rep 2021; 11:12921. [PMID: 34155235 PMCID: PMC8217486 DOI: 10.1038/s41598-021-92196-x] [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: 01/11/2021] [Accepted: 05/31/2021] [Indexed: 11/12/2022] Open
Abstract
Chimeric antigen receptor (CAR) T cells are engineered cells used in cancer therapy and are studied to treat infectious diseases. Trafficking and persistence of CAR T cells is an important requirement for efficacy to target cancer. Here, we describe a CAR RNA FISH histo-cytometry platform combined with a random reaction seed image analysis algorithm to quantitate spatial distribution and in vivo functional activity of a CAR T cell population at a single cell resolution for preclinical models. In situ, CAR T cell exhibited a heterogenous effector gene expression and this was related to the distance from tumor cells, allowing a quantitative assessment of the potential in vivo effectiveness. The platform offers the potential to study immune functions of genetically engineered cells in situ with their target cells in tissues with high statistical power and thus, can serve as an important tool for preclinical assessment of CAR T cell effectiveness.
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Affiliation(s)
- Karsten Eichholz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, MS E3-300, Seattle, WA, 98190, USA
| | - Alvason Zhenhua Li
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, MS E3-300, Seattle, WA, 98190, USA
| | - Kurt Diem
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Michael Claus Jensen
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, USA.,Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Jia Zhu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, MS E3-300, Seattle, WA, 98190, USA.,Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, MS E3-300, Seattle, WA, 98190, USA. .,Department of Laboratory Medicine, University of Washington, Seattle, WA, USA. .,Department of Medicine, University of Washington, Seattle, WA, USA.
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Barros Ribeiro da Silva V, Porcionatto M, Toledo Ribas V. The Rise of Molecules Able To Regenerate the Central Nervous System. J Med Chem 2019; 63:490-511. [PMID: 31518122 DOI: 10.1021/acs.jmedchem.9b00863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Injury to the adult central nervous system (CNS) usually leads to permanent deficits of cognitive, sensory, and/or motor functions. The failure of axonal regeneration in the damaged CNS limits functional recovery. The lack of information concerning the biological mechanism of axonal regeneration and its complexity has delayed the process of drug discovery for many years compared to other drug classes. Starting in the early 2000s, the ability of many molecules to stimulate axonal regrowth was evaluated through automated screening techniques; many hits and some new mechanisms involved in axonal regeneration were identified. In this Perspective, we discuss the rise of the CNS regenerative drugs, the main biological techniques used to test these drug candidates, some of the most important screens performed so far, and the main challenges following the identification of a drug that is able to induce axonal regeneration in vivo.
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Affiliation(s)
| | - Marimélia Porcionatto
- Universidade Federal de São Paulo , Escola Paulista de Medicina, Laboratório de Neurobiologia Molecular, Departmento de Bioquímica , Rua Pedro de Toledo, 669 - third floor, 04039-032 São Paulo , São Paolo , Brazil
| | - Vinicius Toledo Ribas
- Universidade Federal de Minas Gerais , Instituto de Ciências Biológicas, Departamento de Morfologia, Laboratório de Neurobiologia Av. Antônio Carlos, 6627, room O3-245 , - Campus Pampulha, 31270-901 , Belo Horizonte , Minas Gerais , Brazil
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