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Saliba N, Gagliano G, Gustavsson AK. Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.27.559876. [PMID: 37808751 PMCID: PMC10557638 DOI: 10.1101/2023.09.27.559876] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Multi-target single-molecule super-resolution fluorescence microscopy offers a powerful means of understanding the distributions and interplay between multiple subcellular structures at the nanoscale. However, single-molecule super-resolution imaging of whole mammalian cells is often hampered by high fluorescence background and slow acquisition speeds, especially when imaging multiple targets in 3D. In this work, we have mitigated these issues by developing a steerable, dithered, single-objective tilted light sheet for optical sectioning to reduce fluorescence background and a pipeline for 3D nanoprinting microfluidic systems for reflection of the light sheet into the sample. This easily adaptable novel microfluidic fabrication pipeline allows for the incorporation of reflective optics into microfluidic channels without disrupting efficient and automated solution exchange. By combining these innovations with point spread function engineering for nanoscale localization of individual molecules in 3D, deep learning for analysis of overlapping emitters, active 3D stabilization for drift correction and long-term imaging, and Exchange-PAINT for sequential multi-target imaging without chromatic offsets, we demonstrate whole-cell multi-target 3D single-molecule super-resolution imaging with improved precision and imaging speed.
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Affiliation(s)
- Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, 77005
| | - Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, 77005
- Smalley-Curl Institute, Rice University, Houston, TX, 77005
- Applied Physics Program, Rice University, Houston, TX, 77005
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, 77005
- Smalley-Curl Institute, Rice University, Houston, TX, 77005
- Department of BioSciences, Rice University, Houston, TX, 77005
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, 77005
- Center for Nanoscale Imaging Sciences, Rice University, Houston, TX, 77005
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030
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Kramer SN, Antarasen J, Reinholt CR, Kisley L. A practical guide to light-sheet microscopy for nanoscale imaging: Looking beyond the cell. JOURNAL OF APPLIED PHYSICS 2024; 136:091101. [PMID: 39247785 PMCID: PMC11380115 DOI: 10.1063/5.0218262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/12/2024] [Indexed: 09/10/2024]
Abstract
We present a comprehensive guide to light-sheet microscopy (LSM) to assist scientists in navigating the practical implementation of this microscopy technique. Emphasizing the applicability of LSM to image both static microscale and nanoscale features, as well as diffusion dynamics, we present the fundamental concepts of microscopy, progressing through beam profile considerations, to image reconstruction. We outline key practical decisions in constructing a home-built system and provide insight into the alignment and calibration processes. We briefly discuss the conditions necessary for constructing a continuous 3D image and introduce our home-built code for data analysis. By providing this guide, we aim to alleviate the challenges associated with designing and constructing LSM systems and offer scientists new to LSM a valuable resource in navigating this complex field.
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Affiliation(s)
- Stephanie N Kramer
- Department of Physics, Case Western Reserve University, Rockefeller Building, 2076 Adelbert Road, Cleveland, Ohio 44106, USA
| | - Jeanpun Antarasen
- Department of Physics, Case Western Reserve University, Rockefeller Building, 2076 Adelbert Road, Cleveland, Ohio 44106, USA
| | - Cole R Reinholt
- Department of Physics, Case Western Reserve University, Rockefeller Building, 2076 Adelbert Road, Cleveland, Ohio 44106, USA
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Ascheid D, Baumann M, Pinnecker J, Friedrich M, Szi-Marton D, Medved C, Bundalo M, Ortmann V, Öztürk A, Nandigama R, Hemmen K, Ergün S, Zernecke A, Hirth M, Heinze KG, Henke E. A vascularized breast cancer spheroid platform for the ranked evaluation of tumor microenvironment-targeted drugs by light sheet fluorescence microscopy. Nat Commun 2024; 15:3599. [PMID: 38678014 PMCID: PMC11055956 DOI: 10.1038/s41467-024-48010-z] [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: 11/28/2023] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
Targeting the supportive tumor microenvironment (TME) is an approach of high interest in cancer drug development. However, assessing TME-targeted drug candidates presents a unique set of challenges. We develop a comprehensive screening platform that allows monitoring, quantifying, and ranking drug-induced effects in self-organizing, vascularized tumor spheroids (VTSs). The confrontation of four human-derived cell populations makes it possible to recreate and study complex changes in TME composition and cell-cell interaction. The platform is modular and adaptable for tumor entity or genetic manipulation. Treatment effects are recorded by light sheet fluorescence microscopy and translated by an advanced image analysis routine in processable multi-parametric datasets. The system proved to be robust, with strong interassay reliability. We demonstrate the platform's utility for evaluating TME-targeted antifibrotic and antiangiogenic drugs side-by-side. The platform's output enabled the differential evaluation of even closely related drug candidates according to projected therapeutic needs.
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Affiliation(s)
- David Ascheid
- Institute of Anatomy and Cell Biology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Magdalena Baumann
- Institute of Anatomy and Cell Biology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Jürgen Pinnecker
- Chair of Molecular Microscopy, Rudolf-Virchow-Center for Integrative and Translational Bioimaging, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Mike Friedrich
- Chair of Molecular Microscopy, Rudolf-Virchow-Center for Integrative and Translational Bioimaging, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Daniel Szi-Marton
- Institute of Anatomy and Cell Biology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Cornelia Medved
- Institute of Anatomy and Cell Biology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Maja Bundalo
- Institute of Experimental Biomedicine, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Vanessa Ortmann
- Institute of Anatomy and Cell Biology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Asli Öztürk
- Institute of Anatomy and Cell Biology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Rajender Nandigama
- Institute of Anatomy and Cell Biology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
- Max Planck Institute of Heart and Lung Research, Bad Nauheim, Germany
| | - Katherina Hemmen
- Chair of Molecular Microscopy, Rudolf-Virchow-Center for Integrative and Translational Bioimaging, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Süleymann Ergün
- Institute of Anatomy and Cell Biology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Alma Zernecke
- Institute of Experimental Biomedicine, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Matthias Hirth
- Institut für Medientechnik, Technische Universität Illmenau, Illmenau, Germany
| | - Katrin G Heinze
- Chair of Molecular Microscopy, Rudolf-Virchow-Center for Integrative and Translational Bioimaging, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
| | - Erik Henke
- Institute of Anatomy and Cell Biology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
- Graduate School for Life Sciences, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
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Shi Y, Tabet JS, Milkie DE, Daugird TA, Yang CQ, Ritter AT, Giovannucci A, Legant WR. Smart lattice light-sheet microscopy for imaging rare and complex cellular events. Nat Methods 2024; 21:301-310. [PMID: 38167656 PMCID: PMC11216155 DOI: 10.1038/s41592-023-02126-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024]
Abstract
Light-sheet microscopes enable rapid high-resolution imaging of biological specimens; however, biological processes span spatiotemporal scales. Moreover, long-term phenotypes are often instigated by rare or fleeting biological events that are difficult to capture with a single imaging modality. Here, to overcome this limitation, we present smartLLSM, a microscope that incorporates artificial intelligence-based instrument control to autonomously switch between epifluorescent inverted imaging and lattice light-sheet microscopy (LLSM). We apply this approach to two unique processes: cell division and immune synapse formation. In each context, smartLLSM provides population-level statistics across thousands of cells and autonomously captures multicolor three-dimensional datasets or four-dimensional time-lapse movies of rare events at rates that dramatically exceed human capabilities. From this, we quantify the effects of Taxol dose on spindle structure and kinetochore dynamics in dividing cells and of antigen strength on cytotoxic T lymphocyte engagement and lytic granule polarization at the immune synapse. Overall, smartLLSM efficiently detects rare events within heterogeneous cell populations and records these processes with high spatiotemporal four-dimensional imaging over statistically significant replicates.
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Affiliation(s)
- Yu Shi
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jimmy S Tabet
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Timothy A Daugird
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chelsea Q Yang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Andrea Giovannucci
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Wesley R Legant
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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