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Clearing and Labeling Techniques for Large-Scale Biological Tissues
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  • Journal title : Molecules and Cells
  • Volume 39, Issue 6,  2016, pp.439-446
  • Publisher : Korea Society for Molecular and Cellular Biology
  • DOI : 10.14348/molcells.2016.0088
 Title & Authors
Clearing and Labeling Techniques for Large-Scale Biological Tissues
Seo, Jinyoung; Choe, Minjin; Kim, Sung-Yon;
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 Abstract
Clearing and labeling techniques for large-scale biological tissues enable simultaneous extraction of molecular and structural information with minimal disassembly of the sample, facilitating the integration of molecular, cellular and systems biology across different scales. Recent years have witnessed an explosive increase in the number of such methods and their applications, reflecting heightened interest in organ-wide clearing and labeling across many fields of biology and medicine. In this review, we provide an overview and comparison of existing clearing and labeling techniques and discuss challenges and opportunities in the investigations of large-scale biological systems.
 Keywords
3D volume imaging;CLARITY;large-scale tissue clearing;stochastic electrotransport;SWITCH;whole-mount labeling;
 Language
English
 Cited by
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Synapsin-based approaches to brain plasticity in adult social insects, Current Opinion in Insect Science, 2016, 18, 27  crossref(new windwow)
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Genetically encoded indicators of neuronal activity, Nature Neuroscience, 2016, 19, 9, 1142  crossref(new windwow)
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Methods for Evaluating the Stimuli-Responsive Delivery of Nucleic Acid and Gene Medicines, CHEMICAL & PHARMACEUTICAL BULLETIN, 2017, 65, 7, 642  crossref(new windwow)
 References
1.
Aoyagi, Y., Kawakami, R., Osanai, H., Hibi, T., and Nemoto, T. (2015). A rapid optical clearing protocol using 2,2'-thiodiethanol for microscopic observation of fixed mouse brain. Plos One 10, e0116280. crossref(new window)

2.
Bolin, F.P., Preuss, L.E., Taylor, R.C., and Ference, R.J. (1989). Refractive index of some mammalian tissues using a fiber optic cladding method. Appl. Opt. 28, 2297. crossref(new window)

3.
Choi, B., Tsu, L., Chen, E., Ishak, T.S., Iskandar, S.M., Chess, S., and Nelson, J.S. (2005). Determination of chemical agent optical clearing potential using in vitro human skin. Lasers Surg. Med. 36, 72-75. crossref(new window)

4.
Choi, H.M.T., Chang, J.Y., Trinh, L.A., Padilla, J.E., Fraser, S.E., and Pierce, N.A. (2010). Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat. Biotechnol. 28, 1208-1212. crossref(new window)

5.
Choi, H.M.T., Beck, V.A., and Pierce, N.A. (2014). Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability. ACS Nano 8, 4284-4294. crossref(new window)

6.
Chung, K., Wallace, J., Kim, S.-Y., Kalyanasundaram, S., Andalman, A.S., Davidson, T.J., Mirzabekov, J.J., Zalocusky, K.A., Mattis, J., Denisin, A.K., et al. (2013). Structural and molecular interrogation of intact biological systems. Nature 497, 332-337. crossref(new window)

7.
Costantini, I., Ghobril, J.-P., Di Giovanna, A.P., Mascaro, A.L.A., Silvestri, L., Mullenbroich, M.C., Onofri, L., Conti, V., Vanzi, F., Sacconi, L., et al. (2015). A versatile clearing agent for multimodal brain imaging. Sci. Rep. 5, 9808. crossref(new window)

8.
Dodt, H.-U., Leischner, U., Schierloh, A., Jahrling, N., Mauch, C.P., Deininger, K., Deussing, J.M., Eder, M., Zieglgansberger, W., and Becker, K. (2007). Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat. Methods 4, 331-336. crossref(new window)

9.
Economo, M.N., Clack, N.G., Lavis, L.D., Gerfen, C.R., Svoboda, K., Myers, E.W., and Chandrashekar, J. (2016). A platform for brain-wide imaging and reconstruction of individual neurons. eLife 5, e10566.

10.
Erturk, A., Becker, K., Jahrling, N., Mauch, C.P., Hojer, C.D., Egen, J.G., Hellal, F., Bradke, F., Sheng, M., and Dodt, H.-U. (2012a). Three-dimensional imaging of solvent-cleared organs using 3DISCO. Nat. Protoc. 7, 1983-1995. crossref(new window)

11.
Erturk, A., Mauch, C.P., Hellal, F., Forstner, F., Keck, T., Becker, K., Jahrling, N., Steffens, H., Richter, M., Hubener, M., et al. (2012b). Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury. Nat. Med. 18, 166-171. crossref(new window)

12.
Gleave, J.A., Lerch, J.P., Henkelman, R.M., and Nieman, B.J. (2013). A method for 3D immunostaining and optical imaging of the mouse brain demonstrated in neural progenitor cells. PloS One 8, e72039-e72039. crossref(new window)

13.
Hama, H., Kurokawa, H., Kawano, H., Ando, R., Shimogori, T., Noda, H., Fukami, K., Sakaue-Sawano, A., and Miyawaki, A. (2011). Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat. Neurosci. 14, 1481-1488. crossref(new window)

14.
Hama, H., Hioki, H., Namiki, K., Hoshida, T., Kurokawa, H., Ishidate, F., Kaneko, T., Akagi, T., Saito, T., Saido, T., et al. (2015). ScaleS: an optical clearing palette for biological imaging. Nat. Neurosci. 18, 1518-1529. crossref(new window)

15.
Hofman, F.M., and Taylor, C.R. (2001). Immunohistochemistry. In current protocols in immunology. (John Wiley & Sons, Inc.).

16.
Hopwood, D. (1972). Theoretical and practical aspects of glutaraldehyde fixation. Histochem. J. 4, 267-303. crossref(new window)

17.
Hua, L., Zhou, R., Thirumalai, D., and Berne, B.J. (2008). Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proc. Natl. Acad. Sci. 105, 16928-16933. crossref(new window)

18.
Huang, D., Swanson, E.A., Lin, C.P., Schuman, J.S., Stinson, W.G., Chang, W., Hee, M.R., Flotte, T., Gregory, K., Puliafito, C.A., et al. (1991). Optical coherence tomography. Science 254, 1178-1181. crossref(new window)

19.
Ke, M.-T., Fujimoto, S., and Imai, T. (2013). SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction. Nat. Neurosci. 16, 1154-1161. crossref(new window)

20.
Keller, P.J., and Ahrens, M.B. (2015). Visualizing whole-brain activity and development at the single-cell level using light-sheet microscopy. Neuron 85, 462-483. crossref(new window)

21.
Kim, S.-Y., Chung, K., and Deisseroth, K. (2013). Light microscopy mapping of connections in the intact brain. Trends Cogn. Sci. 17, 596-599. crossref(new window)

22.
Kim, S.-Y., Cho, J.H., Murray, E., Bakh, N., Choi, H., Ohn, K., Ruelas, L., Hubbert, A., McCue, M., Vassallo, S.L., et al. (2015). Stochastic electrotransport selectively enhances the transport of highly electromobile molecules. Proc. Natl. Acad. Sci. U SA 112, E6274-E6283. crossref(new window)

23.
Kurihara, D., Mizuta, Y., Sato, Y., and Higashiyama, T. (2015). ClearSee: a rapid optical clearing reagent for whole-plant fluorescence imaging. Dev. Camb. Engl. 142, 4168-4179.

24.
Kuwajima, T., Sitko, A.A., Bhansali, P., Jurgens, C., Guido, W., and Mason, C. (2013). ClearT: a detergent- and solvent-free clearing method for neuronal and non-neuronal tissue. Development 140, 1364-1368. crossref(new window)

25.
Lee, E., Choi, J., Jo, Y., Kim, J.Y., Jang, Y.J., Lee, H.M., Kim, S.Y., Lee, H.-J., Cho, K., Jung, N., et al. (2016). ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging. Sci. Rep. 6, 18631. crossref(new window)

26.
Long, D.J., and Buggs, C. (2008). Microwave oven-based technique for immunofluorescent staining of paraffin-embedded tissues. J. Mol. Histol. 39, 1-4. crossref(new window)

27.
Mao, Z., Zhu, D., Hu, Y., Wen, X., and Han, Z. (2008). Influence of alcohols on the optical clearing effect of skin in vitro. J. Biomed. Opt. 13, 021104. crossref(new window)

28.
McGurk, L., Morrison, H., Keegan, L.P., Sharpe, J., and O'Connell, M.A. (2007). Three-Dimensional Imaging of Drosophila melanogaster. PLoS One 2, e834. crossref(new window)

29.
Muehllehner, G., and Karp, J.S. (2006). Positron emission tomography. Phys. Med. Biol. 51, R117. crossref(new window)

30.
Murray, E., Cho, J.H., Goodwin, D., Ku, T., Swaney, J., Kim, S.-Y., Choi, H., Park, Y.-G., Park, J.-Y., Hubbert, A., et al. (2015). Simple, scalable proteomic imaging for high-dimensional profiling of intact systems. Cell 163, 1500-1514. crossref(new window)

31.
Pallotto, M., Watkins, P.V., Fubara, B., Singer, J.H., and Briggman, K.L. (2015). Extracellular space preservation aids the connectomic analysis of neural circuits. eLife 4.

32.
Palmer, W.M., Martin, A.P., Flynn, J.R., Reed, S.L., White, R.G., Furbank, R.T., and Grof, C.P.L. (2015). PEA-CLARITY: 3D molecular imaging of whole plant organs. Sci. Rep. 5, 13492. crossref(new window)

33.
Reiser, M.F., Semmler, W., and Hricak, H. (2007). Magnetic Resonance Tomography (Springer Science & Business Media).

34.
Renier, N., Wu, Z., Simon, D.J., Yang, J., Ariel, P., and Tessier-Lavigne, M. (2014). iDISCO: a simple, rapid method to immunolabel large tissue samples for volume Imaging. Cell 159, 896-910. crossref(new window)

35.
Richardson, D.S., and Lichtman, J.W. (2015). Clarifying tissue clearing. Cell 162, 246-257. crossref(new window)

36.
Sillitoe, R.V., and Hawkes, R. (2002). Whole-mount immunohistochemistry: a high-throughput screen for patterning defects in the mouse cerebellum. J. Histochem. Cytochem. 50, 235-244. crossref(new window)

37.
Spalteholz, W. (1914). Uber das Durchsichtigmachen von menschlichen und tierischen Praparaten (Leipzig: S. Hierzel).

38.
Sung, H.-W., Hsu, H.-L., Shih, C.-C., and Lin, D.-S. (1996). Crosslinking characteristics of biological tissues fixed with monofunctional or multifunctional epoxy compounds. Biomaterials 17, 1405-1410. crossref(new window)

39.
Susaki, E.A., and Ueda, H.R. (2016). Whole-body and whole-organ clearing and imaging techniques with single-cell resolution: toward organism-level systems biology in mammals. Cell Chem. Biol. 23, 137-157. crossref(new window)

40.
Susaki, E.A., Tainaka, K., Perrin, D., Kishino, F., Tawara, T., Watanabe, T.M., Yokoyama, C., Onoe, H., Eguchi, M., Yamaguchi, S., et al. (2014). Whole-brain imaging with single-cell resolution using chemical cocktails and computational Analysis. Cell 157, 726-739. crossref(new window)

41.
Susaki, E.A., Tainaka, K., Perrin, D., Yukinaga, H., Kuno, A., and Ueda, H.R. (2015). Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging. Nat. Protoc. 10, 1709-1727. crossref(new window)

42.
Sylwestrak, E.L., Rajasethupathy, P., Wright, M.A., Jaffe, A., and Deisseroth, K. (2016). Multiplexed intact-tissue transcriptional analysis at cellular resolution. Cell 164, 792-804. crossref(new window)

43.
Tainaka, K., Kubota, S.I., Suyama, T.Q., Susaki, E.A., Perrin, D., Ukai-Tadenuma, M., Ukai, H., and Ueda, H.R. (2014). Wholebody imaging with single-cell resolution by tissue decolorization. Cell 159, 911-924. crossref(new window)

44.
Tanenbaum, M.E., Gilbert, L.A., Qi, L.S., Weissman, J.S., and Vale, R.D. (2014). A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159, 635-646. crossref(new window)

45.
Tomer, R., Ye, L., Hsueh, B., and Deisseroth, K. (2014). Advanced CLARITY for rapid and high-resolution imaging of intact tissues. Nat. Protoc. 9, 1682-1697. crossref(new window)

46.
Tomer, R., Lovett-Barron, M., Kauvar, I., Andalman, A., Burns, V.M., Sankaran, S., Grosenick, L., Broxton, M., Yang, S., and Deisseroth, K. (2015). SPED light sheet microscopy: fast mapping of biological system structure and function. Cell 163, 1796-1806. crossref(new window)

47.
Tuchin, V.V. (2015). Tissue optics and photonics: light-tissue interaction. J. Biomed. Photonics Eng. 1, 98-134.

48.
Van Essen, D.C., Smith, S.M., Barch, D.M., Behrens, T.E.J., Yacoub, E., and Ugurbil, K. (2013). The WU-Minn human connectome project: an overview. NeuroImage 80, 62-79. crossref(new window)

49.
Warner, C.A., Biedrzycki, M.L., Jacobs, S.S., Wisser, R.J., Caplan, J.L., and Sherrier, D.J. (2014). An optical clearing technique for plant tissues allowing deep imaging and compatible with fluorescence microscopy. Plant Physiol. 166, 1684-1687. crossref(new window)

50.
Yang, B., Treweek, J.B., Kulkarni, R.P., Deverman, B.E., Chen, C.-K., Lubeck, E., Shah, S., Cai, L., and Gradinaru, V. (2014). Single-cell phenotyping within transparent intact tissue through whole-body clearing. Cell 158, 945-958. crossref(new window)