1
|
Schueler J, Sjöman H, Kriesi C. Sensor extended imaging workflow for creating fit for purpose models in basic and applied cell biology. Commun Biol 2024; 7:170. [PMID: 38341479 PMCID: PMC10858951 DOI: 10.1038/s42003-024-05843-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
While various engineering disciplines spent years on developing methods and workflows to increase their R&D efficiency, the field of cell biology has seen limited evolution in the fundamental approaches to interact with living cells. Perturbations are mostly of chemical nature, and physiologically relevant contexts and stimuli are left with limited attention, resulting in a solution space constrained within the boundaries of presently manageable perturbations. To predict in the laboratory how a drug will work in a human patient, cell biology must have a closer look at life and strive to mimic the human being in all his complexity. By implementing an iterative process from perturbation to measurement and vice versa, the authors suggest using a sensor-extended imaging workflow to implement product development practices to cell biology, opening a physiologically relevant solution space for the development of truly translational and predictive fit for purpose in vitro cell models.
Collapse
Affiliation(s)
- Julia Schueler
- Charles River Germany GmbH, Am Flughafen 12-14, 79111, Freiburg, Germany.
| | - Heikki Sjöman
- Vitroscope AS, Leirfossvegen 5d, 7037, Trondheim, Norway
| | - Carlo Kriesi
- Vitroscope AS, Leirfossvegen 5d, 7037, Trondheim, Norway
| |
Collapse
|
2
|
Stossi F, Singh PK, Safari K, Marini M, Labate D, Mancini MA. High throughput microscopy and single cell phenotypic image-based analysis in toxicology and drug discovery. Biochem Pharmacol 2023; 216:115770. [PMID: 37660829 DOI: 10.1016/j.bcp.2023.115770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023]
Abstract
Measuring single cell responses to the universe of chemicals (drugs, natural products, environmental toxicants etc.) is of paramount importance to human health as phenotypic variability in sensing stimuli is a hallmark of biology that is considered during high throughput screening. One of the ways to approach this problem is via high throughput, microscopy-based assays coupled with multi-dimensional single cell analysis methods. Here, we will summarize some of the efforts in this vast and growing field, focusing on phenotypic screens (e.g., Cell Painting), single cell analytics and quality control, with particular attention to environmental toxicology and drug screening. We will discuss advantages and limitations of high throughput assays with various end points and levels of complexity.
Collapse
Affiliation(s)
- Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA.
| | - Pankaj K Singh
- GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA; Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Kazem Safari
- GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA; Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Michela Marini
- GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA; Department of Mathematics, University of Houston, Houston, TX, USA
| | - Demetrio Labate
- GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA; Department of Mathematics, University of Houston, Houston, TX, USA
| | - Michael A Mancini
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; GCC Center for Advanced Microscopy and Image Informatics, Houston, TX, USA; Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| |
Collapse
|
3
|
Zhang K, Pan J, Yu Y. Regulation of Neural Circuitry under General Anesthesia: New Methods and Findings. Biomolecules 2022; 12:biom12070898. [PMID: 35883456 PMCID: PMC9312763 DOI: 10.3390/biom12070898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 02/01/2023] Open
Abstract
General anesthesia has been widely utilized since the 1840s, but its underlying neural circuits remain to be completely understood. Since both general anesthesia and sleep are reversible losses of consciousness, studies on the neural-circuit mechanisms affected by general anesthesia have mainly focused on the neural nuclei or the pathways known to regulate sleep. Three advanced technologies commonly used in neuroscience, in vivo calcium imaging, chemogenetics, and optogenetics, are used to record and modulate the activity of specific neurons or neural circuits in the brain areas of interest. Recently, they have successfully been used to study the neural nuclei and pathways of general anesthesia. This article reviews these three techniques and their applications in the brain nuclei or pathways affected by general anesthesia, to serve as a reference for further and more accurate exploration of other neural circuits under general anesthesia and to contribute to other research fields in the future.
Collapse
Affiliation(s)
- Kai Zhang
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin 300052, China; (K.Z.); (J.P.)
- Tianjin Institute of Anesthesiology, Tianjin 300052, China
| | - Jiacheng Pan
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin 300052, China; (K.Z.); (J.P.)
- Tianjin Institute of Anesthesiology, Tianjin 300052, China
| | - Yonghao Yu
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin 300052, China; (K.Z.); (J.P.)
- Tianjin Institute of Anesthesiology, Tianjin 300052, China
- Correspondence:
| |
Collapse
|
4
|
Hartmann J, Wong M, Gallo E, Gilmour D. An image-based data-driven analysis of cellular architecture in a developing tissue. eLife 2020; 9:e55913. [PMID: 32501214 PMCID: PMC7274788 DOI: 10.7554/elife.55913] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/24/2020] [Indexed: 12/22/2022] Open
Abstract
Quantitative microscopy is becoming increasingly crucial in efforts to disentangle the complexity of organogenesis, yet adoption of the potent new toolbox provided by modern data science has been slow, primarily because it is often not directly applicable to developmental imaging data. We tackle this issue with a newly developed algorithm that uses point cloud-based morphometry to unpack the rich information encoded in 3D image data into a straightforward numerical representation. This enabled us to employ data science tools, including machine learning, to analyze and integrate cell morphology, intracellular organization, gene expression and annotated contextual knowledge. We apply these techniques to construct and explore a quantitative atlas of cellular architecture for the zebrafish posterior lateral line primordium, an experimentally tractable model of complex self-organized organogenesis. In doing so, we are able to retrieve both previously established and novel biologically relevant patterns, demonstrating the potential of our data-driven approach.
Collapse
Affiliation(s)
- Jonas Hartmann
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Mie Wong
- Institute of Molecular Life Sciences, University of Zurich (UZH)ZurichSwitzerland
| | - Elisa Gallo
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Institute of Molecular Life Sciences, University of Zurich (UZH)ZurichSwitzerland
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of BiosciencesHeidelbergGermany
| | - Darren Gilmour
- Institute of Molecular Life Sciences, University of Zurich (UZH)ZurichSwitzerland
| |
Collapse
|
5
|
Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration. Nat Commun 2019; 10:4059. [PMID: 31492853 PMCID: PMC6731298 DOI: 10.1038/s41467-019-12046-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/19/2019] [Indexed: 02/06/2023] Open
Abstract
HIV-1 recurrently targets active genes and integrates in the proximity of the nuclear pore compartment in CD4+ T cells. However, the genomic features of these genes and the relevance of their transcriptional activity for HIV-1 integration have so far remained unclear. Here we show that recurrently targeted genes are proximal to super-enhancer genomic elements and that they cluster in specific spatial compartments of the T cell nucleus. We further show that these gene clusters acquire their location during the activation of T cells. The clustering of these genes along with their transcriptional activity are the major determinants of HIV-1 integration in T cells. Our results provide evidence of the relevance of the spatial compartmentalization of the genome for HIV-1 integration, thus further strengthening the role of nuclear architecture in viral infection.
Collapse
|
6
|
Chessel A, Carazo Salas RE. From observing to predicting single-cell structure and function with high-throughput/high-content microscopy. Essays Biochem 2019; 63:197-208. [PMID: 31243141 PMCID: PMC6610450 DOI: 10.1042/ebc20180044] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023]
Abstract
In the past 15 years, cell-based microscopy has evolved its focus from observing cell function to aiming to predict it. In particular-powered by breakthroughs in computer vision, large-scale image analysis and machine learning-high-throughput and high-content microscopy imaging have enabled to uniquely harness single-cell information to systematically discover and annotate genes and regulatory pathways, uncover systems-level interactions and causal links between cellular processes, and begin to clarify and predict causal cellular behaviour and decision making. Here we review these developments, discuss emerging trends in the field, and describe how single-cell 'omics and single-cell microscopy are imminently in an intersecting trajectory. The marriage of these two fields will make possible an unprecedented understanding of cell and tissue behaviour and function.
Collapse
Affiliation(s)
- Anatole Chessel
- École polytechnique, Université Paris-Saclay, 91128 Palaiseau Cedex, France
| | | |
Collapse
|
7
|
|
8
|
Abstract
The long linear chromosomes of eukaryotic organisms are tightly packed into the nucleus of the cell. Beyond a first organization into nucleosomes and higher-order chromatin fibers, the positioning of nuclear DNA within the three-dimensional space of the nucleus plays a critical role in genome function and gene expression. Different techniques have been developed to assess nanoscale chromatin organization, nuclear position of genomic regions or specific chromatin features and binding proteins as well as higher-order chromatin organization. Here, I present an overview of imaging and molecular techniques applied to study nuclear architecture in plants, with special attention to the related protocols published in the "Plant Chromatin Dynamics" edition from Methods in Molecular Biology.
Collapse
Affiliation(s)
- Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001, Clermont-Ferrand, France.
| |
Collapse
|
9
|
Pegoraro G, Misteli T. High-Throughput Imaging for the Discovery of Cellular Mechanisms of Disease. Trends Genet 2017; 33:604-615. [PMID: 28732598 DOI: 10.1016/j.tig.2017.06.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/19/2017] [Accepted: 06/20/2017] [Indexed: 12/23/2022]
Abstract
High-throughput imaging (HTI) is a powerful tool in the discovery of cellular disease mechanisms. While traditional approaches to identify disease pathways often rely on knowledge of the causative genetic defect, HTI-based screens offer an unbiased discovery approach based on any morphological or functional defects of disease cells or tissues. In this review, we provide an overview of the use of HTI for the study of human disease mechanisms. We discuss key technical aspects of HTI and highlight representative examples of its practical applications for the discovery of molecular mechanisms of disease, focusing on infectious diseases and host-pathogen interactions, cancer, and rare genetic diseases. We also present some of the current challenges and possible solutions offered by novel cell culture systems and genome engineering approaches.
Collapse
Affiliation(s)
- Gianluca Pegoraro
- NCI High-Throughput Imaging Facility, Bethesda, MD 20892, USA; Center for Cancer Research, National Cancer Institute/NIH, Bethesda, MD 20892, USA.
| | - Tom Misteli
- Center for Cancer Research, National Cancer Institute/NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
10
|
Do M, Isaacson SA, McDermott G, Le Gros MA, Larabell CA. Imaging and characterizing cells using tomography. Arch Biochem Biophys 2015; 581:111-21. [PMID: 25602704 PMCID: PMC4506273 DOI: 10.1016/j.abb.2015.01.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/29/2014] [Accepted: 01/11/2015] [Indexed: 12/11/2022]
Abstract
We can learn much about cell function by imaging and quantifying sub-cellular structures, especially if this is done non-destructively without altering said structures. Soft X-ray tomography (SXT) is a high-resolution imaging technique for visualizing cells and their interior structure in 3D. A tomogram of the cell, reconstructed from a series of 2D projection images, can be easily segmented and analyzed. SXT has a very high specimen throughput compared to other high-resolution structure imaging modalities; for example, tomographic data for reconstructing an entire eukaryotic cell is acquired in a matter of minutes. SXT visualizes cells without the need for chemical fixation, dehydration, or staining of the specimen. As a result, the SXT reconstructions are close representations of cells in their native state. SXT is applicable to most cell types. The deep penetration of soft X-rays allows cells, even mammalian cells, to be imaged without being sectioned. Image contrast in SXT is generated by the differential attenuation soft X-ray illumination as it passes through the specimen. Accordingly, each voxel in the tomographic reconstruction has a measured linear absorption coefficient (LAC) value. LAC values are quantitative and give rise to each sub-cellular component having a characteristic LAC profile, allowing organelles to be identified and segmented from the milieu of other cell contents. In this chapter, we describe the fundamentals of SXT imaging and how this technique can answer real world questions in the study of the nucleus. We also describe the development of correlative methods for the localization of specific molecules in a SXT reconstruction. The combination of fluorescence and SXT data acquired from the same specimen produces composite 3D images, rich with detailed information on the inner workings of cells.
Collapse
Affiliation(s)
- Myan Do
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Samuel A Isaacson
- Department of Mathematics and Statistics, Boston University, Boston, MA 02215, United States
| | - Gerry McDermott
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Mark A Le Gros
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Carolyn A Larabell
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
| |
Collapse
|
11
|
Burman B, Misteli T, Pegoraro G. Quantitative detection of rare interphase chromosome breaks and translocations by high-throughput imaging. Genome Biol 2015; 16:146. [PMID: 26313373 PMCID: PMC4531802 DOI: 10.1186/s13059-015-0718-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We report a method for the sensitive detection of rare chromosome breaks and translocations in interphase cells. HiBA-FISH (High-throughput break-apart FISH) combines high-throughput imaging with the measurement of the spatial separation of FISH probes flanking target genome regions of interest. As proof-of-principle, we apply hiBA-FISH to detect with high sensitivity and specificity rare chromosome breaks and translocations in the anaplastic large cell lymphoma breakpoint regions of NPM1 and ALK. This method complements existing approaches to detect translocations by overcoming the need for precise knowledge of translocation breakpoints and it extends traditional FISH by its quantitative nature.
Collapse
Affiliation(s)
- Bharat Burman
- Cell Biology of Genomes, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Program in Cell, Molecular, and Developmental Biology, Tufts University Sackler School of Biomedical Sciences, Boston, MA, 02111, USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Gianluca Pegoraro
- NCI High-Throughput Imaging Facility, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
12
|
The Histochemistry and Cell Biology pandect: the year 2014 in review. Histochem Cell Biol 2015; 143:339-68. [PMID: 25744491 DOI: 10.1007/s00418-015-1313-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2015] [Indexed: 02/07/2023]
Abstract
This review encompasses a brief synopsis of the articles published in 2014 in Histochemistry and Cell Biology. Out of the total of 12 issues published in 2014, two special issues were devoted to "Single-Molecule Super-Resolution Microscopy." The present review is divided into 11 categories, providing an easy format for readers to quickly peruse topics of particular interest to them.
Collapse
|