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Abstract
Expansion microscopy (ExM) is a technique that physically expands preserved cells and tissues before microscope imaging, so that conventional diffraction-limited microscopes can perform nanoscale-resolution imaging. In ExM, biomolecules or their markers are linked to a dense, swellable gel network synthesized throughout a specimen. Mechanical homogenization of the sample (e.g., by protease digestion) and the addition of water enable isotropic swelling of the gel, so that the relative positions of biomolecules are preserved. We previously presented ExM protocols for analyzing proteins and RNAs in cells and tissues. Here we describe a cookbook-style ExM protocol for expanding cultured HeLa cells with immunostained microtubules, aimed to help newcomers familiarize themselves with the experimental setups and skills required to successfully perform ExM. Our aim is to help beginners, or students in a wet-lab classroom setting, learn all the key steps of ExM. © 2020 The Authors.
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Affiliation(s)
- Chi Zhang
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts
| | - Jeong Seuk Kang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts
| | - Shoh M Asano
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Current address, Internal Medicine Research Unit, Pfizer Inc., Cambridge, Massachusetts
| | - Ruixuan Gao
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Department of Biological Engineering, MIT, Cambridge, Massachusetts.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts.,Koch Institute for Cancer Research, MIT, Cambridge, Massachusetts
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Gao R, Asano SM, Upadhyayula S, Pisarev I, Milkie DE, Liu TL, Singh V, Graves A, Huynh GH, Zhao Y, Bogovic J, Colonell J, Ott CM, Zugates C, Tappan S, Rodriguez A, Mosaliganti KR, Sheu SH, Pasolli HA, Pang S, Xu CS, Megason SG, Hess H, Lippincott-Schwartz J, Hantman A, Rubin GM, Kirchhausen T, Saalfeld S, Aso Y, Boyden ES, Betzig E. Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution. Science 2019; 363:eaau8302. [PMID: 30655415 PMCID: PMC6481610 DOI: 10.1126/science.aau8302] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/30/2018] [Indexed: 12/20/2022]
Abstract
Optical and electron microscopy have made tremendous inroads toward understanding the complexity of the brain. However, optical microscopy offers insufficient resolution to reveal subcellular details, and electron microscopy lacks the throughput and molecular contrast to visualize specific molecular constituents over millimeter-scale or larger dimensions. We combined expansion microscopy and lattice light-sheet microscopy to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entire Drosophila brain. These included synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly brain region. The technology should enable statistically rich, large-scale studies of neural development, sexual dimorphism, degree of stereotypy, and structural correlations to behavior or neural activity, all with molecular contrast.
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Affiliation(s)
- Ruixuan Gao
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Shoh M Asano
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
| | - Srigokul Upadhyayula
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 200 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Igor Pisarev
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Tsung-Li Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ved Singh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Austin Graves
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Grace H Huynh
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Yongxin Zhao
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - John Bogovic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jennifer Colonell
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Carolyn M Ott
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Christopher Zugates
- arivis AG, 1875 Connecticut Avenue NW, 10th floor, Washington, DC 20009, USA
| | - Susan Tappan
- MBF Bioscience, 185 Allen Brook Lane, Suite 101, Williston, VT 05495, USA
| | - Alfredo Rodriguez
- MBF Bioscience, 185 Allen Brook Lane, Suite 101, Williston, VT 05495, USA
| | - Kishore R Mosaliganti
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Shu-Hsien Sheu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - H Amalia Pasolli
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Song Pang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Harald Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | | | - Adam Hantman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Gerald M Rubin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Tom Kirchhausen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 200 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Yoshinori Aso
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Edward S Boyden
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
- MIT Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
- Koch Institute, MIT, Cambridge, MA 02139, USA
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Physics, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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3
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Asano SM, Gao R, Wassie AT, Tillberg PW, Chen F, Boyden ES. Expansion Microscopy: Protocols for Imaging Proteins and RNA in Cells and Tissues. ACTA ACUST UNITED AC 2018; 80:e56. [PMID: 30070431 DOI: 10.1002/cpcb.56] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Expansion microscopy (ExM) is a recently developed technique that enables nanoscale-resolution imaging of preserved cells and tissues on conventional diffraction-limited microscopes via isotropic physical expansion of the specimens before imaging. In ExM, biomolecules and/or fluorescent labels in the specimen are linked to a dense, expandable polymer matrix synthesized evenly throughout the specimen, which undergoes 3-dimensional expansion by ∼4.5 fold linearly when immersed in water. Since our first report, versions of ExM optimized for visualization of proteins, RNA, and other biomolecules have emerged. Here we describe best-practice, step-by-step ExM protocols for performing analysis of proteins (protein retention ExM, or proExM) as well as RNAs (expansion fluorescence in situ hybridization, or ExFISH), using chemicals and hardware found in a typical biology lab. Furthermore, a detailed protocol for handling and mounting expanded samples and for imaging them with confocal and light-sheet microscopes is provided. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Shoh M Asano
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Internal Medicine Research Unit, Pfizer Inc., Cambridge, Massachusetts
| | - Ruixuan Gao
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts
| | - Asmamaw T Wassie
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Department of Biological Engineering, MIT, Cambridge, Massachusetts
| | | | - Fei Chen
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Department of Biological Engineering, MIT, Cambridge, Massachusetts.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts.,Koch Institute, MIT, Cambridge, Massachusetts
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