Expansion microscopy: principles and uses in biological research.


Journal

Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604

Informations de publication

Date de publication:
01 2019
Historique:
received: 15 02 2018
accepted: 10 10 2018
entrez: 22 12 2018
pubmed: 24 12 2018
medline: 25 6 2019
Statut: ppublish

Résumé

Many biological investigations require 3D imaging of cells or tissues with nanoscale spatial resolution. We recently discovered that preserved biological specimens can be physically expanded in an isotropic fashion through a chemical process. Expansion microscopy (ExM) allows nanoscale imaging of biological specimens with conventional microscopes, decrowds biomolecules in support of signal amplification and multiplexed readout chemistries, and makes specimens transparent. We review the principles of how ExM works, advances in the technology made by our group and others, and its applications throughout biology and medicine.

Identifiants

pubmed: 30573813
doi: 10.1038/s41592-018-0219-4
pii: 10.1038/s41592-018-0219-4
pmc: PMC6373868
mid: NIHMS1010719
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Review

Langues

eng

Sous-ensembles de citation

IM

Pagination

33-41

Subventions

Organisme : NINDS NIH HHS
ID : R01 NS102727
Pays : United States
Organisme : NHGRI NIH HHS
ID : RM1 HG008525
Pays : United States
Organisme : NIBIB NIH HHS
ID : R01 EB024261
Pays : United States
Organisme : NIMH NIH HHS
ID : R41 MH112318
Pays : United States
Organisme : NINDS NIH HHS
ID : DP1 NS087724
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH110932
Pays : United States

Références

Dunn, R. C. Near-field scanning optical microscopy. Chem. Rev. 99, 2891–2928 (1999).
doi: 10.1021/cr980130e
Dürig, U., Pohl, D. W. & Rohner, F. Near-field optical-scanning microscopy. J. Appl. Phys. 59, 3318–3327 (1986).
doi: 10.1063/1.336848
Hell, S.W. Far-field optical nanoscopy. In Proc. 2010 23rd Annual Meeting of the IEEE Photonics Society (eds Jagadish, C. et al.) 3–4 (IEEE, New York, 2010).
Huang, B., Bates, M. & Zhuang, X. Super-resolution fluorescence microscopy. Annu. Rev. Biochem. 78, 993–1016 (2009).
doi: 10.1146/annurev.biochem.77.061906.092014
Chen, F., Tillberg, P. W. & Boyden, E. S. Expansion microscopy. Science 347, 543–548 (2015).
doi: 10.1126/science.1260088
Tanaka, T. et al. Phase transitions in ionic gels. Phys. Rev. Lett. 45, 1636–1639 (1980).
doi: 10.1103/PhysRevLett.45.1636
Hausen, P. & Dreyer, C. The use of polyacrylamide as an embedding medium for immunohistochemical studies of embryonic tissues. Stain Technol. 56, 287–293 (1981).
doi: 10.3109/10520298109067329
Cohen, Y., Ramon, O., Kopelman, I. J. & Mizrahi, S. Characterization of inhomogeneous polyacrylamide hydrogels. J. Polym. Sci. B Polym. Phys. 30, 1055–1067 (1992).
doi: 10.1002/polb.1992.090300913
Tillberg, P. W. et al. Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies. Nat. Biotechnol. 34, 987–992 (2016).
doi: 10.1038/nbt.3625
Chen, F. et al. Nanoscale imaging of RNA with expansion microscopy. Nat. Methods 13, 679–684 (2016).
doi: 10.1038/nmeth.3899
Chang, J.-B. et al. Iterative expansion microscopy. Nat. Methods 14, 593–599 (2017).
doi: 10.1038/nmeth.4261
Zhao, Y. et al. Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy. Nat. Biotechnol. 35, 757–764 (2017).
doi: 10.1038/nbt.3892
Chozinski, T. J. et al. Expansion microscopy with conventional antibodies and fluorescent proteins. Nat. Methods 13, 485–488 (2016).
doi: 10.1038/nmeth.3833
Ku, T. et al. Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues. Nat. Biotechnol. 34, 973–981 (2016).
doi: 10.1038/nbt.3641
Truckenbrodt, S. et al. X10 expansion microscopy enables 25-nm resolution on conventional microscopes. EMBO Rep. 19, e45836 (2018).
doi: 10.15252/embr.201845836
Tsanov, N. et al. smiFISH and FISH-quant—a flexible single RNA detection approach with super-resolution capability. Nucleic Acids Res. 44, e165 (2016).
doi: 10.1093/nar/gkw784
Asano, S. M. et al. Expansion microscopy: protocols for imaging proteins and RNA in cells and tissues. Curr. Protoc. Cell Biol. 80, e56 (2018).
doi: 10.1002/cpcb.56
Freifeld, L. et al. Expansion microscopy of zebrafish for neuroscience and developmental biology studies. Proc. Natl Acad. Sci. USA 114, E10799–E10808 (2017).
doi: 10.1073/pnas.1706281114
Migliori, B. et al. Light sheet theta microscopy for rapid high-resolution imaging of large biological samples. BMC Biol. 16, 57 (2018).
doi: 10.1186/s12915-018-0521-8
Hama, H. et al. Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat. Neurosci. 14, 1481–1488 (2011).
doi: 10.1038/nn.2928
Susaki, E. A. et al. Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell 157, 726–739 (2014).
doi: 10.1016/j.cell.2014.03.042
Chung, K. et al. Structural and molecular interrogation of intact biological systems. Nature 497, 332–337 (2013).
doi: 10.1038/nature12107
Murakami, T. C. et al. A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing. Nat. Neurosci. 21, 625–637 (2018).
doi: 10.1038/s41593-018-0109-1
Zhang, Y. S. et al. Hybrid microscopy: enabling inexpensive high-performance imaging through combined physical and optical magnifications. Sci. Rep. 6, 22691 (2016).
doi: 10.1038/srep22691
Aoki, T., Tsuchida, S., Yahara, T. & Hamaue, N. Novel assays for proteases using green fluorescent protein-tagged substrate immobilized on a membrane disk. Anal. Biochem. 378, 132–137 (2008).
doi: 10.1016/j.ab.2008.04.022
Nicholls, S. B. & Hardy, J. A. Structural basis of fluorescence quenching in caspase activatable-GFP. Protein Sci. 22, 247–257 (2013).
doi: 10.1002/pro.2188
Deshpande, T. et al. Subcellular reorganization and altered phosphorylation of the astrocytic gap junction protein connexin43 in human and experimental temporal lobe epilepsy. Glia 65, 1809–1820 (2017).
doi: 10.1002/glia.23196
Crittenden, J. R. et al. Striosome-dendron bouquets highlight a unique striatonigral circuit targeting dopamine-containing neurons. Proc. Natl Acad. Sci. USA 113, 11318–11323 (2016).
doi: 10.1073/pnas.1613337113
Decarreau, J. et al. The tetrameric kinesin Kif25 suppresses pre-mitotic centrosome separation to establish proper spindle orientation. Nat. Cell Biol. 19, 384–390 (2017).
doi: 10.1038/ncb3486
Suofu, Y. et al. Dual role of mitochondria in producing melatonin and driving GPCR signaling to block cytochrome c release. Proc. Natl Acad. Sci. USA 114, E7997–E8006 (2017).
doi: 10.1073/pnas.1705768114
Wang, Y. et al. Combined expansion microscopy with structured illumination microscopy for analyzing protein complexes. Nat. Protoc. 13, 1869–1895 (2018).
doi: 10.1038/s41596-018-0023-8
Orth, A. et al. Super-multiplexed fluorescence microscopy via photostability contrast. Biomed. Opt. Express 9, 2943–2954 (2018).
doi: 10.1364/BOE.9.002943
Chozinski, T. J. et al. Volumetric, nanoscale optical imaging of mouse and human kidney via expansion microscopy. Sci. Rep. 8, 10396 (2018).
doi: 10.1038/s41598-018-28694-2
Tsai, A. et al. Nuclear microenvironments modulate transcription from low-affinity enhancers. eLife 6, e28975 (2017).
doi: 10.7554/eLife.28975
Jiang, N. et al. Superresolution imaging of Drosophila tissues using expansion microscopy. Mol. Biol. Cell 29, 1413–1421 (2018).
doi: 10.1091/mbc.E17-10-0583
Cahoon, C. K. et al. Superresolution expansion microscopy reveals the three-dimensional organization of the Drosophila synaptonemal complex. Proc. Natl Acad. Sci. USA 114, E6857–E6866 (2017).
doi: 10.1073/pnas.1705623114
Sümbül, U. et al. Automated scalable segmentation of neurons from multispectral images. In Advances in Neural Information Processing Systems 29 (eds Lee, D. D. et al.) 1912–1920 (NIPS Foundation, La Jolla, CA, 2016).
Mosca, T. J., Luginbuhl, D. J., Wang, I. E. & Luo, L. Presynaptic LRP4 promotes synapse number and function of excitatory CNS neurons. eLife 6, 1–29 (2017).
doi: 10.7554/eLife.27347
Wang, I. E., Lapan, S. W., Scimone, M. L., Clandinin, T. R. & Reddien, P. W. Hedgehog signaling regulates gene expression in planarian glia. eLife 5, e16996 (2016).
doi: 10.7554/eLife.16996
Halpern, A. R., Alas, G. C. M., Chozinski, T. J., Paredez, A. R. & Vaughan, J. C. Hybrid structured illumination expansion microscopy reveals microbial cytoskeleton organization. ACS Nano 11, 12677–12686 (2017).
doi: 10.1021/acsnano.7b07200
Artur, C. G. et al. Plasmonic nanoparticle-based expansion microscopy with surface-enhanced Raman and dark-field spectroscopic imaging. Biomed. Opt. Express 9, 603–615 (2018).
doi: 10.1364/BOE.9.000603
Villaseñor, R., Schilling, M., Sundaresan, J., Lutz, Y. & Collin, L. Sorting tubules regulate blood-brain barrier transcytosis. Cell Rep. 21, 3256–3270 (2017).
doi: 10.1016/j.celrep.2017.11.055
Li, R., Chen, X., Lin, Z., Wang, Y. & Sun, Y. Expansion enhanced nanoscopy. Nanoscale 10, 17552–17556 (2018).
doi: 10.1039/C8NR04267E
Treweek, J. B. et al. Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. Nat. Protoc. 10, 1860–1896 (2015).
doi: 10.1038/nprot.2015.122
Unnersjö-Jess, D. et al. Confocal super-resolution imaging of the glomerular filtration barrier enabled by tissue expansion. Kidney Int. 93, 1008–1013 (2018).
doi: 10.1016/j.kint.2017.09.019
Wei, L. et al. Super-multiplex vibrational imaging. Nature 544, 465–470 (2017).
doi: 10.1038/nature22051
Hu, F. et al. Supermultiplexed optical imaging and barcoding with engineered polyynes. Nat. Methods 15, 194–200 (2018).
doi: 10.1038/nmeth.4578
Kumar, A. et al. Influenza virus exploits tunneling nanotubes for cell-to-cell spread. Sci. Rep. 7, 40360 (2017).
doi: 10.1038/srep40360
Gao, M. et al. Expansion stimulated emission depletion microscopy (ExSTED). ACS Nano 12, 4178–4185 (2018).
doi: 10.1021/acsnano.8b00776
Elmore, J. G. et al. Diagnostic concordance among pathologists interpreting breast biopsy specimens. J. Am. Med. Assoc. 313, 1122–1132 (2015).
doi: 10.1001/jama.2015.1405
Choi, H. M. T. et al. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat. Biotechnol. 28, 1208–1212 (2010).
doi: 10.1038/nbt.1692
Choi, H. M. T., Beck, V. A. & Pierce, N. A. Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability. ACS Nano 8, 4284–4294 (2014).
doi: 10.1021/nn405717p
Lin, R. et al. A hybridization-chain-reaction-based method for amplifying immunosignals. Nat. Methods 15, 275–278 (2018).
doi: 10.1038/nmeth.4611
Lee, J. H. et al. Highly multiplexed subcellular RNA sequencing in situ. Science 343, 1360–1363 (2014).
doi: 10.1126/science.1250212
Ke, R. et al. In situ sequencing for RNA analysis in preserved tissue and cells. Nat. Methods 10, 857–860 (2013).
doi: 10.1038/nmeth.2563
Yoon, Y.-G. et al. Feasibility of 3D reconstruction of neural morphology using expansion microscopy and barcode-guided agglomeration. Front. Comput. Neurosci. 11, 97 (2017).
doi: 10.3389/fncom.2017.00097
Lubeck, E. & Cai, L. Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat. Methods 9, 743–748 (2012).
doi: 10.1038/nmeth.2069
Lubeck, E., Coskun, A. F., Zhiyentayev, T., Ahmad, M. & Cai, L. Single-cell in situ RNA profiling by sequential hybridization. Nat. Methods 11, 360–361 (2014).
doi: 10.1038/nmeth.2892
Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S. & Zhuang, X. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015).
doi: 10.1126/science.aaa6090
Moffitt, J. R. et al. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. Proc. Natl Acad. Sci. USA 113, 11046–11051 (2016).
doi: 10.1073/pnas.1612826113
Wang, G., Moffitt, J. R. & Zhuang, X. Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy. Sci. Rep. 8, 4847 (2018).
doi: 10.1038/s41598-018-22297-7
Shah, S., Lubeck, E., Zhou, W. & Cai, L. In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus. Neuron 92, 342–357 (2016).
doi: 10.1016/j.neuron.2016.10.001
Wang, Y. et al. Rapid sequential in situ multiplexing with DNA-exchange-imaging in neuronal cells and tissues. Nano Lett. 17, 6131–6139 (2017).
doi: 10.1021/acs.nanolett.7b02716

Auteurs

Asmamaw T Wassie (AT)

Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.

Yongxin Zhao (Y)

Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.

Edward S Boyden (ES)

Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. esb@media.mit.edu.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. esb@media.mit.edu.
McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, USA. esb@media.mit.edu.
Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA. esb@media.mit.edu.
Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA. esb@media.mit.edu.
Center for Neurobiological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. esb@media.mit.edu.

Articles similaires

Humans Resilience, Psychological Rhode Island Biomedical Research Stress, Psychological
United States Periodicals as Topic Cross-Sectional Studies Humans Biomedical Research
Microscopy Humans Artificial Intelligence Primary Health Care
Malaria, Vivax Peru Humans Recurrence Female

Classifications MeSH