Fluorescent labeling of abundant reactive entities (FLARE) for cleared-tissue and super-resolution microscopy

Min Yen Lee, Chenyi Mao, Adam K. Glaser, Marcus A. Woodworth, Aaron R. Halpern, Adilijiang Ali, Jonathan T. C. Liu, Joshua C. Vaughan

Published: 2022-02-01 DOI: 10.1038/s41596-021-00667-2

fluorescent labeling

super-resolution microscopy

FLARE

reactive fluorophores

cleared-tissue microscopy

AI 解读

Supplementary information

Supplementary Method 1, Supplementary Figs. 1–4, Supplementary Tables 1 and 2 and the first frame of Supplementary Video 1.

Reporting Summary

Supplementary Video 1

Open-top light-sheet imaging of a ~1-mm-thick mouse kidney section. (Adapted with permission from ref. 3, AAAS, under a Creative Commons license CC BY-NC 4.0.)

Supplementary Code 1

Custom Wolfram Mathematica scripts used for stitching tiling images.

Generation of mouse–human chimeric embryos

Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting

Generation of CRISPR–Cas9-mediated genetic knockout human intestinal tissue–derived enteroid lines by lentivirus transduction and single-cell cloning

A puromycin-dependent activity-based sensing probe for histochemical staining of hydrogen peroxide in cells and animal tissues

Decoding personal biotic and abiotic airborne exposome

A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys

Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds

Biomimetic tail-to-head terpene cyclizations using the resorcin[4]arene capsule catalyst

Neuroscience robotics for controlled induction and real-time assessment of hallucinations

Scanorama: integrating large and diverse single-cell transcriptomic datasets

Single-cell RNA sequencing (scRNA-seq)（单细胞RNA测序）

Data integration（数据集成）

Heterogeneity（异质性）

查看全部

Sections

Figures

References

Supplementary information

Bradbury, A. & Plückthun, A. Reproducibility: standardize antibodies used in research. Nature 518, 27–29 (2015).
Schnell, U., Dijk, F., Sjollema, K. A. & Giepmans, B. N. G. Immunolabeling artifacts and the need for live-cell imaging. Nat. Methods 9, 152–158 (2012).
Mao, C. et al. Feature-rich covalent stains for super-resolution and cleared tissue fluorescence microscopy. Sci. Adv. 6, eaba4542 (2020).
Titford, M. Progress in the development of microscopical techniques for diagnostic pathology. J. Histotechnol. 32, 9–19 (2009).
Sigal, Y. M., Zhou, R. & Zhuang, X. Visualizing and discovering cellular structures with super-resolution microscopy. Science 361, 880–887 (2018).
Schermelleh, L. et al. Super-resolution microscopy demystified. Nat. Cell Biol. 21, 72–84 (2019).
Sahl, S. J., Hell, S. W. & Jakobs, S. Fluorescence nanoscopy in cell biology. Nat. Rev. Mol. Cell Biol. 18, 685–701 (2017).
Chen, F., Tillberg, P. W. & Boyden, E. S. Expansion microscopy. Science 347, 543–548 (2015).
Chozinski, T. J. et al. Expansion microscopy with conventional antibodies and fluorescent proteins. Nat. Methods 13, 485–488 (2016).
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).
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).
Richardson, D. S. & Lichtman, J. W. Clarifying tissue clearing. Cell 162, 246–257 (2015).
Tainaka, K., Kuno, A., Kubota, S. I., Murakami, T. & Ueda, H. R. Chemical principles in tissue clearing and staining protocols for whole-body cell profiling. Annu. Rev. Cell Dev. Biol. 32, 713–741 (2016).
Glaser, A. K. et al. Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues. Nat. Commun. 10, 2781 (2019).
Klingberg, A. et al. Fully automated evaluation of total glomerular number and capillary tuft size in nephritic kidneys using lightsheet microscopy. J. Am. Soc. Nephrol. 28, 453–459 (2017).
Masselink, W. et al. Broad applicability of a streamlined ethyl cinnamate-based clearing procedure. Development 146, dev166884 (2019).
Beliveau, B. J. et al. Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc. Natl Acad. Sci. USA 109, 21301–21306 (2012).
Chen, Y. et al. Rapid pathology of lumpectomy margins with open-top light-sheet (OTLS) microscopy. Biomed. Opt. Express 10, 1257 (2019).
Xie, W. et al. Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins. J. Biomed. Opt. 24, 12 (2019).
Yu, C.-C. et al. Expansion microscopy of C. elegans. eLife 9, e46249 (2020).
M’Saad, O. & Bewersdorf, J. Light microscopy of proteins in their ultrastructural context. Nat. Commun. 11, 3850 (2020).
Damstra, H. G. J. et al. Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx). Preprint at bioRxiv http://doi.org/10.1101/2021.02.03.428837 (2021).
Sim, J. et al. Whole-ExM: expansion microscopy imaging of all anatomical structures of whole larval zebrafish. Preprint at bioRxiv http://doi.org/10.1101/2021.05.18.443629 (2021).
Elfer, K. N. et al. DRAQ5 and eosin (‘D&E’) as an analog to hematoxylin and eosin for rapid fluorescence histology of fresh tissues. PLoS ONE 11, e0165530 (2016).
Serafin, R., Xie, W., Glaser, A. K. & Liu, J. T. C. FalseColor-Python: a rapid intensity-leveling and digital-staining package for fluorescence-based slide-free digital pathology. PLoS ONE 15, e0233198 (2020).
Yun, D. H. et al. Ultrafast immunostaining of organ-scale tissues for scalable proteomic phenotyping. Preprint at bioRxiv http://doi.org/10.1101/660373 (2019).
Ku, T. et al. Elasticizing tissues for reversible shape transformation and accelerated molecular labeling. Nat. Methods 17, 609–613 (2020).
Susaki, E. A. et al. Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues. Nat. Commun. 11, 1982 (2020).
Zhao, S. et al. Cellular and molecular probing of intact human organs. Cell 180, 796–812.e19 (2020).
Bertiaux, E. et al. Expansion microscopy provides new insights into the cytoskeleton of malaria parasites including the conservation of a conoid. PLOS Biol. 19, e3001020 (2021).
Bancroft’s Theory and Practice of Histological Techniques 7th edn (eds Suvarna, S. K. et al.) (Elsevier Churchill Livingstone, 2013).
Apgar et al. Fluorescence microscopy of rat embryo sections stained with haematoxylin-eosin and Masson’s trichrome method: fluorescence microscopy using haematoxylin-eosin and Masson’s trichrome. J. Microsc. 191, 20–27 (1998).
Giacomelli, M. G. et al. Virtual hematoxylin and eosin transillumination microscopy using epi-fluorescence imaging. PLoS ONE 11, e0159337 (2016).
Glaser, A. K. et al. Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens. Nat. Biomed. Eng. 1, 0084 (2017).
Kasten, F. H., Burton, V. & Glover, P. Fluorescent Schiff-type reagents for cytochemical detection of polyaldehyde moieties in sections and smears. Nature 184, 1797–1798 (1959).
Li, Z. et al. Application of periodic acid–Schiff fluorescence emission for immunohistochemistry of living mouse renal glomeruli by an ‘in vivo cryotechnique’. Arch. Histol. Cytol. 69, 147–161 (2006).
Shi, X. et al. Label-retention expansion microscopy. J. Cell Biol. 220, e202105067 (2021).
Karagiannis, E. D. et al. expansion microscopy of lipid membranes. Preprint at bioRxiv http://biorxiv.org/lookup/doi/10.1101/829903 (2019).
Wen, G. et al. Evaluation of direct grafting strategies via trivalent anchoring for enabling lipid membrane and cytoskeleton staining in expansion microscopy. ACS Nano 14, 7860–7867 (2020).
Götz, R. et al. Nanoscale imaging of bacterial infections by sphingolipid expansion microscopy. Nat. Commun. 11, 6173 (2020).
Chang, J.-B. et al. Iterative expansion microscopy. Nat. Methods 14, 593–599 (2017).
Ross, M. H. Histology: A Text and Atlas with Correlated Cell and Molecular Biology (Lippincott Williams & Wilkins, 2006).
Bucur, O. et al. Nanoscale imaging of clinical specimens using conventional and rapid-expansion pathology. Nat. Protoc. http://doi.org/10.1038/s41596-020-0300-1 (2020).
Unnersjö-Jess, D. et al. Confocal super-resolution imaging of the glomeruluar filtration barrier enables by tissue expansion. Kidney Int. http://doi.org/10.1016/j.kint.2017.09.019 (2017).
Hermanson, G. Bioconjugate Techniques 2nd edn (Elsevier, 2008).
Mujumdar, R. B., Ernst, L. A., Mujumdar, S. R., Lewis, C. J. & Waggoner, A. S. Cyanine dye labeling reagents: sulfoindocyanine succinimidyl esters. Bioconjug. Chem. 4, 105–111 (1993).
Murray, E. et al. Simple, scalable proteomic imaging for high-dimensional profiling of intact systems. Cell 163, 1500–1514 (2015).
Chozinski, T. J. et al. Volumetric, nanoscale optical imaging of mouse and human kidney via expansion microscopy. Sci. Rep. http://doi.org/10.1038/s41598-018-28694-2 (2018).
Power, R. M. & Huisken, J. A guide to light-sheet fluorescence microscopy for multiscale imaging. Nat. Methods 14, 360–373 (2017).
Santi, P. A. Light sheet fluorescence microscopy: a review. J. Histochem. Cytochem. 59, 129–138 (2011).
Liu, J. T. C. et al. Harnessing non-destructive 3D pathology. Nat. Biomed. Eng. http://doi.org/10.1038/s41551-020-00681-x (2018).
Jiang, N. et al. Superresolution imaging of Drosophila tissues using expansion microscopy. Mol. Biol. Cell 29, 1413–1421 (2018).
Richter, K. N. et al. Glyoxal as an alternative fixative to formaldehyde in immunostaining and super‐resolution microscopy. EMBO J. http://doi.org/10.15252/embj.201695709 (2017).

Fluorescent labeling of abundant reactive entities (FLARE) for cleared-tissue and super-resolution microscopy

Supplementary information

Supplementary information

Reporting Summary

Supplementary Video 1

Supplementary Code 1

推荐阅读