Abstract
This review delves into the rapidly evolving field of deep tissue imaging at cellular resolution, reviewing popular tissue clearing and staining methods in combination with light-sheet fluorescence microscopy (LSFM) including quantification and three-dimensional visualization tools, the field of applications and perspective, particularly with the focus on preclinical cancer research and drug development. The LSFM technique presented here allows an extremely fast optical sectioning for three-dimensional reconstruction of centimeter-sized tissue samples at cellular resolution. However, optical clearing methods are required to receive optical transparent tissue. Application of either tissue autofluorescence, in vivo fluorescence labeling, endogenous fluorescence or ex vivo whole-mount immunolabeling enables three-dimensional in situ visualization of morphological and functional features of unsectioned whole-mount tissue samples. This powerful and innovative imaging technique opens up a new dimension of tissue analysis providing detailed and comprehensive insights into biology. It enables the investigation of normal and pathological tissue features and disease progression and allows precise monitoring of potential therapeutic interventions in intact biological tissue on a cellular level.
Similar content being viewed by others
References
Alnuami AA, Zeedi B, Qadri SM, Ashraf SS (2008) Oxyradical-induced GFP damage and loss of fluorescence. Int J Biol Macromol 43(2):182–186
Becker K, Jährling N, Kramer ER, Schnorrer F, Dodt HU (2008) Ultramicroscopy: 3D reconstruction of large microscopical specimens. J Biophotonics 1(1):36–42
Becker K, Jährling N, Saghafi S, Weiler R, Dodt HU (2012) Chemical clearing and dehydration of GFP expressing mouse brains. PLoS One 7(3):e33916
Becker K, Jährling N, Saghafi S, Dodt HU (2013) Ultramicroscopy: light-sheet-based microscopy for imaging centimeter-sized objects with micrometer resolution. Cold Spring Harb Protoc 8:704–713
Belle M, Godefroy D, Dominici C, Heitz-Marchaland C, Zelina P, Hellal F, Bradke F, Chedotal A (2014) A simple method for 3D analysis of immunolabeled axonal tracts in a transparent nervous system. Cell Rep 9(4):1191–1201
Bibby MC (2004) Orthotopic models of cancer for preclinical drug evaluation: advantages and disadvantages. Eur J Cancer 40(6):852–857
Breckwoldt MO, Bode J, Kurz FT, Hoffmann A, Ochs K, Ott M, Deumelandt K, Kruwel T, Schwarz D, Fischer M, Helluy X, Milford D, Kirschbaum K, Solecki G, Chiblak S, Abdollahi A, Winkler F, Wick W, Platten M, Heiland S, Bendszus M, Tews B (2016) Correlated magnetic resonance imaging and ultramicroscopy (MR-UM) is a tool kit to assess the dynamics of glioma angiogenesis. Elife 5:e11712
Chung K, Deisseroth K (2013) CLARITY for mapping the nervous system. Nat Methods 10(6):508–513
Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, Deisseroth K (2013) Structural and molecular interrogation of intact biological systems. Nature 497(7449):332–337
Costantini I, Ghobril JP, Di Giovanna AP, Allegra Mascaro AL, Silvestri L, Mullenbroich MC, Onofri L, Conti V, Vanzi F, Sacconi L, Guerrini R, Markram H, Iannello G, Pavone FS (2015) A versatile clearing agent for multi-modal brain imaging. Sci Rep 5:9808
Dobosz M, Ntziachristos V, Scheuer W, Strobel S (2014) Multispectral fluorescence ultramicroscopy: three-dimensional visualization and automatic quantification of tumor morphology, drug penetration, and antiangiogenic treatment response. Neoplasia 16(1):1–13
Dodt HU, Leischner U, Schierloh A, Jährling N, Mauch CP, Deininger K, Deussing JM, Eder M, Zieglgansberger W, Becker K (2007) Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat Methods 4(4):331–336
Epp JR, Niibori Y, Liz Hsiang HL, Mercaldo V, Deisseroth K, Josselyn SA, Frankland PW (2015) Optimization of CLARITY for clearing whole-brain and other intact organs(1,2,3). eNeuro. doi:10.1523/ENEURO.0022-15.2015
Ertürk A, Bradke F (2013) High-resolution imaging of entire organs by 3-dimensional imaging of solvent cleared organs (3DISCO). Exp Neurol 242:57–64
Ertürk A, Becker K, Jährling N, Mauch CP, Hojer CD, Egen JG, Hellal F, Bradke F, Sheng M, Dodt HU (2012a) Three-dimensional imaging of solvent-cleared organs using 3DISCO. Nat Protoc 7(11):1983–1995
Ertürk A, Mauch CP, Hellal F, Forstner F, Keck T, Becker K, Jährling N, Steffens H, Richter M, Hubener M, Kramer E, Kirchhoff F, Dodt HU, Bradke F (2012b) Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury. Nat Med 18(1):166–171
Ertürk A, Lafkas D, Chalouni C (2014) Imaging cleared intact biological systems at a cellular level by 3DISCO. J Vis Exp. doi:10.3791/51382
Frese KK, Tuveson DA (2007) Maximizing mouse cancer models. Nat Rev Cancer 7(9):645–658
Fuchs E, Jaffe JS, Long RA, Azam F (2002) Thin laser light sheet microscope for microbial oceanography. Opt Express 10(2):145–154
Hägerling R, Pollmann C, Andreas M, Schmidt C, Nurmi H, Adams RH, Alitalo K, Andresen V, Schulte-Merker S, Kiefer F (2013) A novel multistep mechanism for initial lymphangiogenesis in mouse embryos based on ultramicroscopy. EMBO J 32(5):629–644
Hama H, Kurokawa H, Kawano H, Ando R, Shimogori T, Noda H, Fukami K, Sakaue-Sawano A, Miyawaki A (2011) Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat Neurosci 14(11):1481–1488
Hama H, Hioki H, Namiki K, Hoshida T, Kurokawa H, Ishidate F, Kaneko T, Akagi T, Saito T, Saido T, Miyawaki A (2015) ScaleS: an optical clearing palette for biological imaging. Nat Neurosci 18(10):1518
Harma V, Virtanen J, Makela R, Happonen A, Mpindi JP, Knuuttila M, Kohonen P, Lotjonen J, Kallioniemi O, Nees M (2010) A comprehensive panel of three-dimensional models for studies of prostate cancer growth, invasion and drug responses. PLoS One 5(5):e10431
He X, Gao J, Gambhir SS, Cheng Z (2010) Near-infrared fluorescent nanoprobes for cancer molecular imaging: status and challenges. Trends Mol Med 16(12):574–583
Hoffman RM (2005) The multiple uses of fluorescent proteins to visualize cancer in vivo. Nat Rev Cancer 5(10):796–806
Hoffman RM (2015) Application of GFP imaging in cancer. Lab Invest 95(4):432–452
Hoos A (2016) Development of immuno-oncology drugs—from CTLA4 to PD1 to the next generations. Nat Rev Drug Discov 15(4):235–247
Horton NG, Wang K, Kobat D, Clark CG, Wise FW, Schaffer CB, Xu C (2013) Three-photon microscopy of subcortical structures within an intact mouse brain. Nat Photonics 7(3):205–209
Hou B, Zhang D, Zhao S, Wei M, Yang Z, Wang S, Wang J, Zhang X, Liu B, Fan L, Li Y, Qiu Z, Zhang C, Jiang T (2015) Scalable and DiI-compatible optical clearance of the mammalian brain. Front Neuroanat 9:19
Huisken J, Stainier DY (2009) Selective plane illumination microscopy techniques in developmental biology. Development 136(12):1963–1975
Huisken J, Swoger J, Del Bene F, Wittbrodt J, Stelzer EH (2004) Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 305(5686):1007–1009
Jährling N, Becker K, Dodt HU (2009) 3D-reconstruction of blood vessels by ultramicroscopy. Organogenesis 5(4):227–230
Jobsis FF (1977) Non-invasive, infra-red monitoring of cerebral O2 sufficiency, bloodvolume, HbO2-Hb shifts and bloodflow. Acta Neurol Scand Suppl 64:452–453
Ke MT, Imai T (2014) Optical clearing of fixed brain samples using SeeDB. Curr Protoc Neurosci 66:2–22
Ke MT, Fujimoto S, Imai T (2013) SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction. Nat Neurosci 16(8):1154–1161
Ke MT, Nakai Y, Fujimoto S, Takayama R, Yoshida S, Kitajima TS, Sato M, Imai T (2016) Super-resolution mapping of neuronal circuitry with an index-optimized clearing agent. Cell Rep 14(11):2718–2732
Kim SY, Chung K, Deisseroth K (2013) Light microscopy mapping of connections in the intact brain. Trends Cogn Sci 17(12):596–599
Kobayashi H, Choyke PL (2011) Target-cancer-cell-specific activatable fluorescence imaging probes: rational design and in vivo applications. Acc Chem Res 44(2):83–90
Kolesova H, Capek M, Radochova B, Janacek J, Sedmera D (2016) Comparison of different tissue clearing methods and 3D imaging techniques for visualization of GFP-expressing mouse embryos and embryonic hearts. Histochem Cell Biol 146(2):141–152
Kuwajima T, Sitko AA, Bhansali P, Jurgens C, Guido W, Mason C (2013) ClearT: a detergent- and solvent-free clearing method for neuronal and non-neuronal tissue. Development 140(6):1364–1368
Lee S, Xie J, Chen X (2010) Activatable molecular probes for cancer imaging. Curr Top Med Chem 10(11):1135–1144
Lee E, Choi J, Jo Y, Kim JY, Jang YJ, Lee HM, Kim SY, Lee HJ, Cho K, Jung N, Hur EM, Jeong SJ, Moon C, Choe Y, Rhyu IJ, Kim H, Sun W (2016) ACT-PRESTO: rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging. Sci Rep 6:18631
Leischner U, Zieglgansberger W, Dodt HU (2009) Resolution of ultramicroscopy and field of view analysis. PLoS One 4(6):e5785
Leischner U, Schierloh A, Zieglgansberger W, Dodt HU (2010) Formalin-induced fluorescence reveals cell shape and morphology in biological tissue samples. PLoS One 5(4):e10391
Mendler CT, Feuchtinger A, Heid I, Aichler M, D’Alessandria C, Pirsig S, Blechert B, Wester HJ, Braren R, Walch A, Skerra A, Schwaiger M (2016) Tumor uptake of anti-CD20 fabs depends on tumor perfusion. J Nucl Med [Epub ahead of print]
Menzel R (2011) Ultramicroscopy—imaging a whole animal or a whole brain with micron resolution. Front Neurosci 5:11
Minchinton AI, Tannock IF (2006) Drug penetration in solid tumours. Nat Rev Cancer 6(8):583–592
Moy AJ, Lo PC, Choi B (2013) High-resolution visualization of mouse cardiac microvasculature using optical histology. Biomed Opt Express 5(1):69–77
Moy AJ, Capulong BV, Saager RB, Wiersma MP, Lo PC, Durkin AJ, Choi B (2015) Optical properties of mouse brain tissue after optical clearing with FocusClear (TM). J Biomed Opt 20(9):95010
Müller MG, Georgakoudi I, Zhang Q, Wu J, Feld MS (2001) Intrinsic fluorescence spectroscopy in turbid media: disentangling effects of scattering and absorption. Appl Opt 40(25):4633–4646
Munos-Cháuli R (2013) Getting more CLARITY to gain the third dimension. Eur J Anat 17(4):257–258
Murray E, Cho JH, Goodwin D, Ku T, Swaney J, Kim SY, Choi H, Park YG, Park JY, Hubbert A, McCue M, Vassallo S, Bakh N, Frosch MP, Wedeen VJ, Seung HS, Chung K (2015) Simple, scalable proteomic imaging for high-dimensional profiling of intact systems. Cell 163(6):1500–1514
Ntziachristos V (2006) Fluorescence molecular imaging. Annu Rev Biomed Eng 8:1–33
Ntziachristos V, Ripoll J, Wang LV, Weissleder R (2005) Looking and listening to light: the evolution of whole-body photonic imaging. Nat Biotechnol 23(3):313–320
Page DB, Postow MA, Callahan MK, Allison JP, Wolchok JD (2014) Immune modulation in cancer with antibodies. Annu Rev Med 65:185–202
Pampaloni F, Ansari N, Stelzer EH (2013) High-resolution deep imaging of live cellular spheroids with light-sheet-based fluorescence microscopy. Cell Tissue Res 352(1):161–177
Pampaloni F, Chang BJ, Stelzer EH (2015) Light sheet-based fluorescence microscopy (LSFM) for the quantitative imaging of cells and tissues. Cell Tissue Res 360(1):129–141
Pöschinger T, Renner A, Eisa F, Dobosz M, Strobel S, Weber TG, Brauweiler R, Kalender WA, Scheuer W (2014) Dynamic contrast-enhanced micro-computed tomography correlates with 3-dimensional fluorescence ultramicroscopy in antiangiogenic therapy of breast cancer xenografts. Invest Radiol 49(7):445–456
Renier N, Wu Z, Simon DJ, Yang J, Ariel P, Tessier-Lavigne M (2014) iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging. Cell 159(4):896–910
Richardson DS, Lichtman JW (2015) Clarifying Tissue Clearing. Cell 162(2):246–257
Robertson RT, Levine ST, Haynes SM, Gutierrez P, Baratta JL, Tan ZQ, Longmuir KJ (2015) Use of labeled tomato lectin for imaging vasculature structures. Histochem Cell Biol 143(2):225–234
Santi PA (2011) Light sheet fluorescence microscopy: a review. J Histochem Cytochem 59(2):129–138
Schwarz MK, Scherbarth A, Sprengel R, Engelhardt J, Theer P, Giese G (2015) Fluorescent-protein stabilization and high-resolution imaging of cleared, intact mouse brains. PLoS One 10(5):e0124650
Sharma P, Allison JP (2015) The future of immune checkpoint therapy. Science 348(6230):56–61
Siedentopf H, Zsigmondy R (1903) Über Sichtbarmachung und Größenbestimmung ultramikroskopischer Teilchen, mit besonderer Anwendung auf Goldrubingläser. Ann Phys 10:1–39
Spalteholz W (1914) Über das Durchsichtigmachen von menschlichen und tierischen Präparaten. S Hierzel, Leipzig
Susaki EA, Ueda HR (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(1):137–157
Susaki EA, Tainaka K, Perrin D, Kishino F, Tawara T, Watanabe TM, Yokoyama C, Onoe H, Eguchi M, Yamaguchi S, Abe T, Kiyonari H, Shimizu Y, Miyawaki A, Yokota H, Ueda HR (2014) Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell 157(3):726–739
Susaki EA, Tainaka K, Perrin D, Yukinaga H, Kuno A, Ueda HR (2015) Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging. Nat Protoc 10(11):1709–1727
Tainaka K, Kubota SI, Suyama TQ, Susaki EA, Perrin D, Ukai-Tadenuma M, Ukai H, Ueda HR (2014) Whole-body imaging with single-cell resolution by tissue decolorization. Cell 159(4):911–924
Tainaka K, Kuno A, Kubota SI, Murakami T, Ueda HR (2016) Chemical principles in tissue clearing and staining protocols for whole-body cell profiling. Annu Rev Cell Dev Biol [Epub ahead of print]
Tomer R, Khairy K, Keller PJ (2011) Shedding light on the system: studying embryonic development with light sheet microscopy. Curr Opin Genet Dev 21(5):558–565
Tomer R, Ye L, Hsueh B, Deisseroth K (2014) Advanced CLARITY for rapid and high-resolution imaging of intact tissues. Nat Protoc 9(7):1682–1697
Treweek JB, Chan KY, Flytzanis NC, Yang B, Deverman BE, Greenbaum A, Lignell A, Xiao C, Cai L, Ladinsky MS, Bjorkman PJ, Bjorkman CC, Gradinaru V (2015) Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. Nat Protoc 10(11):1860–1896
Voie AH, Burns DH, Spelman FA (1993) Orthogonal-plane fluorescence optical sectioning: three-dimensional imaging of macroscopic biological specimens. J Microsc 170(Pt 3):229–236
Weissleder R, Ntziachristos V (2003) Shedding light onto live molecular targets. Nat Med 9(1):123–128
Yagublu V, Ahmadova Z, Hafner M, Keese M (2012) Review: fluorescent protein-based tumor models. Vivo 26(4):599–607
Yang B, Treweek JB, Kulkarni RP, Deverman BE, Chen CK, Lubeck E, Shah S, Cai L, Gradinaru V (2014) Single-cell phenotyping within transparent intact tissue through whole-body clearing. Cell 158(4):945–958
Acknowledgments
The authors gratefully acknowledge the financial support of the Deutsche Forschungsgemeinschaft (SFB 824 TP Z02). The authors AF and AW would like to thank Ulrike Buchholz, Claudia-Mareike Pflüger and Andreas Voss for excellent technical assistance. The author MD would like to thank Hadassah Sade, Thomas Pöschinger and Frank Herting for helpful discussion and constant support and the Roche Postdoc Fellowship Program for financing this work.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors AF and AW declare no conflict of interest. The author MD is an employee of Roche Diagnostics GmbH.
Additional information
This review article is dedicated to Professor emeritus Detlev Drenckhahn for his outstanding achievements in the field of histochemistry and cell biology.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Morphology of a mouse lung (cleared according to 3DISCO) based on autofluorescence signals visualized by arivis Vision4D (AVI 140067 kb)
Video 2
2D visualization of virtual tissue slices obtained from different fluorescence channels. First channel: Tumor morphology (autofluorescence, gray). Second channel: Tumor vasculature (Lectin-Alexa647, green). Third channel: Antibody penetration (Trastuzumab-Alexa750, red) (MP4 26017 kb)
Rights and permissions
About this article
Cite this article
Feuchtinger, A., Walch, A. & Dobosz, M. Deep tissue imaging: a review from a preclinical cancer research perspective. Histochem Cell Biol 146, 781–806 (2016). https://doi.org/10.1007/s00418-016-1495-7
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00418-016-1495-7