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Imaging the Mammary Gland and Mammary Tumours in 3D: Optical Tissue Clearing and Immunofluorescence Methods Bethan Lloyd-Lewis1*† , Felicity M

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Imaging the Mammary Gland and Mammary Tumours in 3D: Optical Tissue Clearing and Immunofluorescence Methods Bethan Lloyd-Lewis1*† , Felicity M Lloyd-Lewis, B., Davis, F. M., Harris, O. B., Hitchcock, J. R., Lourenco, F. C., Pasche, M., & Watson, C. J. (2016). Imaging the mammary gland and mammary tumours in 3D; optical tissue clearing and immunofluorescence methods. Breast Cancer Research, 18(1), [127 (2016)]. https://doi.org/10.1186/s13058-016-0754-9 Publisher's PDF, also known as Version of record License (if available): CC BY Link to published version (if available): 10.1186/s13058-016-0754-9 Link to publication record in Explore Bristol Research PDF-document This is the final published version of the article (version of record). It first appeared online via Springer Nature at https://breast-cancer-research.biomedcentral.com/articles/10.1186/s13058-016-0754-9 . Please refer to any applicable terms of use of the publisher. University of Bristol - Explore Bristol Research General rights This document is made available in accordance with publisher policies. Please cite only the published version using the reference above. Full terms of use are available: http://www.bristol.ac.uk/red/research-policy/pure/user-guides/ebr-terms/ Lloyd-Lewis et al. Breast Cancer Research (2016) 18:127 DOI 10.1186/s13058-016-0754-9 RESEARCHARTICLE Open Access Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods Bethan Lloyd-Lewis1*† , Felicity M. Davis1,2*† , Olivia B. Harris1,3, Jessica R. Hitchcock1, Filipe C. Lourenco4, Mathias Pasche5 and Christine J. Watson1,3* Abstract Background: High-resolution 3D imaging of intact tissue facilitates cellular and subcellular analyses of complex structures within their native environment. However, difficulties associated with immunolabelling and imaging fluorescent proteins deep within whole organs have restricted their applications to thin sections or processed tissue preparations, precluding comprehensive and rapid 3D visualisation. Several tissue clearing methods have been established to circumvent issues associated with depth of imaging in opaque specimens. The application of these techniques to study the elaborate architecture of the mouse mammary gland has yet to be investigated. Methods: Multiple tissue clearing methods were applied to intact virgin and lactating mammary glands, namely 3D imaging of solvent-cleared organs, see deep brain (seeDB), clear unobstructed brain imaging cocktails (CUBIC) and passive clarity technique. Using confocal, two-photon and light sheet microscopy, their compatibility with whole- mount immunofluorescent labelling and 3D imaging of mammary tissue was examined. In addition, their suitability for the analysis of mouse mammary tumours was also assessed. Results: Varying degrees of optical transparency, tissue preservation and fluorescent signal conservation were observed between the different clearing methods. SeeDB and CUBIC protocols were considered superior for volumetric fluorescence imaging and whole-mount histochemical staining, respectively. Techniques were compatible with 3D imaging on a variety of platforms, enabling visualisation of mammary ductal and lobulo-alveolar structures at vastly improved depths in cleared tissue. Conclusions: The utility of whole-organ tissue clearing protocols was assessed in the mouse mammary gland. Most methods utilised affordable and widely available reagents, and were compatible with standard confocal microscopy. These techniques enable high-resolution, 3D imaging and phenotyping of mammary cells and tumours in situ, and will significantly enhance our understanding of both normal and pathological mammary gland development. Keywords: Mammary gland, Lactation, Breast cancer, Tissue clearing, 3D imaging, Fluorescence microscopy, Light sheet fluorescence microscopy, Two-photon microscopy * Correspondence: [email protected]; [email protected]; [email protected] †Equal contributors 1Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK Full list of author information is available at the end of the article © The Author(s). 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Lloyd-Lewis et al. Breast Cancer Research (2016) 18:127 Page 2 of 17 Background 3DISCO [8] is based on earlier clearing methods that The mammary gland is composed of a branching epithe- use high-index organic solvents such as benzyl alcohol lial ductal network deeply embedded within a vascu- benzyl benzoate (BABB) [12, 13], and can be combined larised stromal matrix made up of adipocytes, fibroblasts with optimised whole-mount immunolabelling proce- and immune cells [1]. Due to its capacity for rapid dures (termed iDISCO) [14]. To date, 3DISCO remains growth and regeneration, the mouse mammary gland is the only method previously applied to mammary tissue, a powerful model in which to study a range of develop- albeit superficially [8]. PACT [11] relies on hydrogel em- mental processes associated with tissue morphogenesis bedding to stabilise cellular structures prior to tissue and remodelling, and provides important insights into delipidation using ionic detergents. Due to the need for the perturbations that give rise to breast cancer [1]. custom electrophoresis equipment, CLARITY [15] is diffi- However, visualisation of the complex cellular networks cult to implement and can lead to heat-induced tissue within the intact mammary epithelium is greatly im- damage and epitope loss [11]. The PACT protocol cir- peded by the lipid-rich and optically opaque nature of cumvents these issues, relying instead on passive diffusion. this organ. As a result, immunolabelling and fluores- Furthermore, PACT utilises more economical RI match- cence imaging of mammary tissue has traditionally been ing solutions (RIMS and sRIMS), an additional benefit performed using thin tissue sections with assumptions over CLARITY. CUBIC [10] is a urea-based clearing re- about the architectural context and uniformity of a par- agent that includes aminoalcohols and detergents to re- ticular 2D plane. Whilst 3D imaging has recently been move lipids and homogenise RIs within tissue. In addition, used to investigate mammary stem cell dynamics [2–4] CUBIC reagents decolourise blood by eluting the heme and binucleated cells in lactational alveoli [5], these chromophore, further enhancing optical transparency by studies have relied on tissue microdissection [2, 5] minimising light absorption [16]. Finally, SeeDB [9] is a or enzymatic digestion [3]. Consequently, visualisation of water-based optical clearing agent that utilises saturated the mammary epithelial tree at single-cell resolution solutions of fructose and alpha-thioglycerol (which limits within its native stroma remains a fundamental challenge autofluorescence) for RI matching. in mammary gland research. We compared these four protocols for optical transpar- The utility of rendering tissue optically transparent has ency and tissue preservation in the intact mammary gland, been appreciated for over a century [6]. However, recent in addition to their compatibility with immunofluorescent advances in fluorescence microscopy have heralded the labelling and 3D imaging of mammary epithelial cells. development of numerous whole-organ tissue clearing Their suitability for the analysis of mammary tumours was methods aimed at improving optical access and depth of also investigated. Using standard confocal and advanced imaging in intact specimens (reviewed in [7]). These imaging techniques, ductal and lobulo-alveolar structures methods are primarily based on mitigating light scatter- could be readily visualised in cleared tissue, with varying ing caused by heterogeneous cellular components with degrees of fluorescent signal preservation between the dif- different refractive indices (RIs). Techniques broadly rely ferent methods. Overall, our results placed SeeDB and either on organic solvent-based or hydrophilic reagent- CUBIC as methods of choice for high-resolution fluores- based clearing solutions to homogenise RIs within tis- cence imaging and whole-mount histochemical staining of sue, and may also include prior hydrogel embedding mammary glands. The ability to visualise the mammary to stabilise cellular structures. Whilst many protocols epithelial tree at single cell resolution within its native were originally optimised for the central nervous sys- stroma will provide invaluable insight into mammary tem and whole embryos, recent refinements in tissue gland development and tumourigenesis. clearing techniques have facilitated exceptional optical access to many other mammalian tissues. However, Methods the application of these techniques to the mammary Reagents and antibodies gland is yet to be explored. The following reagents were purchased from Sigma Here, we describe the application of four leading tissue Aldrich: neutral buffered formalin (NBF), dimethyl clearing protocols, namely three-dimensional imaging sulfoxide (DMSO), tetrahydrofuran (THF), dichloro- of solvent-cleared organs (3DISCO) [8], see deep brain methane (DCM), dibenzyl ether (DBE), benzyl alcohol, (SeeDB) [9], clear unobstructed
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