Part of this work was conducted through collaboration with Prof. Hiroki R. Ueda (University of Tokyo), Prof. Etsuo A. Susaki (Juntendo University), Prof. Tetsuhiro Tanaka (Tohoku University), Prof. Masafumi Fukagawa, Dr. Takehiko Wada, and Dr. Hirotaka Komaba (Tokai University).

All experiments were approved by the University of Tokyo Institutional Review Board. All animal procedures were performed according to the National Institutes of Health guidelines. Male C57BL/6NJcl mice, 8 weeks old, were used for the present study. The mice were obtained from commercial sources (see Table of Materials).
1. Animal preparation and kidney fixation
<ol>
	<li>Perform perfusion fixation following the steps below.
	<ol>
		<li>Anesthetize the mouse by inhalation of isoflurane (3%, 2.0 L/min) and intraperitoneal administration of medetomidine hydrochloride (0.3 mg/kg), butorphanol tartrate (5 mg/kg), and midazolam (4 mg/kg) (see Table of Materials).</li>
		<li>Perfuse the animal with 20 mL of PBS (pH 7.4) and 30 mL of 4% PFA in phosphate buffer (PB) through the left ventricle of the heart12.</li>
	</ol>
	</li>
	<li>Perform the immersion fixation just after the perfusion fixation and kidney sampling9.
	<ol>
		<li>Immerse the kidney in 4% PFA at 4 &#176;C for an additional 16 h, then wash it with PBS for 2 h (three times)9 (Figure 1). 
		&#8203;CAUTION: Formaldehyde and paraformaldehyde are toxic irritants. Handle reagents in a fume hood with appropriate personal protective equipment.</li>
	</ol>
	</li>
</ol>
2. Decolorization and delipidation
<ol>
	<li>Prepare CUBIC-L for decolorization and delipidation consisting of 10 wt% of Triton X-100 and 10 wt% of N-buthyldiethanolamine (see Table of Materials), following previously published reports4,8,9.</li>
	<li>Perform decolorization and delipidation by CUBIC-L following the steps below.
	<ol>
		<li>Immerse the fixed kidney in 7 mL of 50% (v/v) CUBIC-L (1:1 mixture of water and CUBIC-L) in a 14 mL round bottom tube (see Table of Materials) with gentle shaking at room temperature for 6 h (Figure 2A). Then, immerse it in 7 mL of CUBIC-L in a 14 mL round bottom tube with gentle shaking at 37 &#176;C for 5 days.</li>
		<li>Refresh CUBIC-L every day during this process. After the decolorization and delipidation process, wash the kidney with PBS at room temperature for 2 h (three times)9 (Figure 1). Use a dispensing spoon for sample handling (Figure 2B).</li>
	</ol>
	</li>
</ol>
3. Whole-mount immunofluorescent staining
<ol>
	<li>Prepare the staining buffers.
	<ol>
		<li>Prepare the staining buffer for primary antibodies by mixing 0.5% (v/v) Triton X-100, 0.5% casein in PBS, and 0.05% sodium azide9.</li>
		<li>Prepare the staining buffer for secondary antibodies by mixing 0.5% (v/v) Triton X-100, 0.1% casein in PBS, and 0.05% sodium azide9.</li>
	</ol>
	</li>
	<li>Perform staining with primary antibodies.
	<ol>
		<li>Immunostain the delipidated kidney with primary antibodies (1:100 or 1:200, see Table of Materials) in the staining buffer at 37 &#176;C with gentle shaking for 7 days. 
		NOTE: The amount of the staining buffer needed for one kidney is 500-600 &#181;L (Figure 2C).</li>
		<li>Wash the kidney with 0.5% (v/v) Triton X-100 in PBS (PBST) at room temperature for 1 day9 (Figure 1).</li>
	</ol>
	</li>
	<li>Perform staining with secondary antibodies.
	<ol>
		<li>Immunostain the kidney with secondary antibodies (1:100 or 1:200, see Table of Materials) in the staining buffer at 37 &#176;C with gentle shaking for 7 days. Wash the kidney with PBST at room temperature for 1 day9 (Figure 1).</li>
		<li>Post fixation9, immerse the kidney in 1% formaldehyde in PB (1:36 mixture of 37% formaldehyde and PB) for 3 h, and wash it with PBS at room temperature for 6 h (Figure 1).</li>
	</ol>
	</li>
</ol>
4. Refractive index (RI) matching
<ol>
	<li>Prepare CUBIC-R+.
	<ol>
		<li>Prepare CUBIC-R by mixing 45 wt% of 2,3-dimethyl-1-phenyl-5-pyrazolone/antipyrine and 30 wt% of nicotinamide (see Table of Materials).</li>
		<li>Prepare CUBIC-R+ for refractive index (RI) matching by adding 0.5 v% of N-buthyldiethanolamine to CUBIC-R following the previously published reports4,8,9.</li>
	</ol>
	</li>
	<li>Perform the RI matching.
	<ol>
		<li>Immerse the kidney in 7 mL of 50% (v/v) CUBIC-R+ (1:1 mixture of water and CUBIC-R+) in a 14 mL round bottom tube with gentle shaking at room temperature for 1 day. Then, immerse it in 7 mL of CUBIC-R+ in a 14 mL round bottom tube with gentle shaking at room temperature for 2 days9 (Figure 1). 
		NOTE: Although the kidney floats in 50% CUBIC-R+ at the beginning of the RI matching, it sinks and becomes transparent in CUBIC-R+ at the end of the process (Figure 2D).</li>
	</ol>
	</li>
</ol>
5. Image acquisition and reconstruction
<ol>
	<li>Immerse the RI-matched kidney in a mixture of silicon oil (RI = 1.555) and mineral oil (RI = 1.467) (55:45) during image acquisition (RI = 1.51)5 (Figure 3).</li>
	<li>Acquire 3D images of the whole kidney with a custom-built9 light-sheet fluorescent microscope (see Table of Materials). Collect all raw image data in a 16-bit TIFF format. Visualize and capture the 3D-rendered images with the imaging analysis software (Imaris, see Table of Materials).</li>
</ol>

<ol><li>Velez-Fort, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((The+stimulus+selectivity+and+connectivity+of+layer+six+principal+cells+reveals+cortical+microcircuits+underlying+visual+processing%5BTitle%5D)+AND+%22Neuron%22%5BJournal%5D)">The stimulus selectivity and connectivity of layer six principal cells reveals cortical microcircuits underlying visual processing.</a> Neuron. 83 (6), 1431-1443 (2014).</li>
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<li>Erturk, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Three-dimensional+imaging+of+solvent-cleared+organs+using+3DISCO%5BTitle%5D)+AND+%22Nature+Protocols%22%5BJournal%5D)">Three-dimensional imaging of solvent-cleared organs using 3DISCO.</a> Nature Protocols. 7 (11), 1983-1995 (2012).</li>
<li>Tainaka, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Chemical+Landscape+for+Tissue+Clearing+Based+on+Hydrophilic+Reagents%5BTitle%5D)+AND+%22Cell+Reports%22%5BJournal%5D)">Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents.</a> Cell Reports. 24 (8), 2196-2210 (2018).</li>
<li>Susaki, E. A., Ueda, H. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Whole-body+and+whole-organ+clearing+and+imaging+techniques+with+single-cell+resolution%3A+toward+organism-level+systems+biology+in+mammals%5BTitle%5D)+AND+%22Cell+Chemical+Biology%22%5BJournal%5D)">Whole-body and whole-organ clearing and imaging techniques with single-cell resolution: toward organism-level systems biology in mammals.</a> Cell Chemical Biology. 23 (1), 137-157 (2016).</li>
<li>Keller, P. J., Dodt, H. U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Light+sheet+microscopy+of+living+or+cleared+specimens%5BTitle%5D)+AND+%22Current+Opinion+in+Neurobiology%22%5BJournal%5D)">Light sheet microscopy of living or cleared specimens.</a> Current Opinion in Neurobiology. 22 (1), 138-143 (2012).</li>
<li>Susaki, E. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Advanced+CUBIC+protocols+for+whole-brain+and+whole-body+clearing+and+imaging%5BTitle%5D)+AND+%22Nature+Protocols%22%5BJournal%5D)">Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging.</a> Nature Protocols. 10 (11), 1709-1727 (2015).</li>
<li>Kubota, S. I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Whole-body+profiling+of+cancer+metastasis+with+single-cell+resolution%5BTitle%5D)+AND+%22Cell+Reports%22%5BJournal%5D)">Whole-body profiling of cancer metastasis with single-cell resolution.</a> Cell Reports. 20 (1), 236-250 (2017).</li>
<li>Hasegawa, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Comprehensive+three-dimensional+analysis+%28CUBIC-kidney%29+visualizes+abnormal+renal+sympathetic+nerves+after+ischemia%2Freperfusion+injury%5BTitle%5D)+AND+%22Kidney+International%22%5BJournal%5D)">Comprehensive three-dimensional analysis (CUBIC-kidney) visualizes abnormal renal sympathetic nerves after ischemia/reperfusion injury.</a> Kidney International. 96 (1), 129-138 (2019).</li>
<li>Hasegawa, S., Inoue, T., Inagi, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Neuroimmune+interactions+and+kidney+disease%5BTitle%5D)+AND+%22Kidney+Research+and+Clinical+Practice%22%5BJournal%5D)">Neuroimmune interactions and kidney disease.</a> Kidney Research and Clinical Practice. 38 (3), 282-294 (2019).</li>
<li>Hasegawa, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((The+oral+hypoxia-inducible+factor+prolyl+hydroxylase+inhibitor+enarodustat+counteracts+alterations+in+renal+energy+metabolism+in+the+early+stages+of+diabetic+kidney+disease%5BTitle%5D)+AND+%22Kidney+International%22%5BJournal%5D)">The oral hypoxia-inducible factor prolyl hydroxylase inhibitor enarodustat counteracts alterations in renal energy metabolism in the early stages of diabetic kidney disease.</a> Kidney International. 97 (5), 934-950 (2020).</li>
<li>Gage, G. J., Kipke, D. R., Shain, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Whole+animal+perfusion+fixation+for+rodents%5BTitle%5D)+AND+%22Journal+of+Visualized+Experiments%22%5BJournal%5D)">Whole animal perfusion fixation for rodents.</a> Journal of Visualized Experiments. (65), e3564(2012).</li>
<li>Hasegawa, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Activation+of+sympathetic+signaling+in+macrophages+blocks+systemic+inflammation+and+protects+against+renal+ischemia-reperfusion+injury%5BTitle%5D)+AND+%22Journal+of+the+American+Society+of+Nephrology%22%5BJournal%5D)">Activation of sympathetic signaling in macrophages blocks systemic inflammation and protects against renal ischemia-reperfusion injury.</a> Journal of the American Society of Nephrology. 32 (7), 1599-1615 (2021).</li>
<li>Renier, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((iDISCO%3A+a+simple%2C+rapid+method+to+immunolabel+large+tissue+samples+for+volume+imaging%5BTitle%5D)+AND+%22Cell%22%5BJournal%5D)">iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging.</a> Cell. 159 (4), 896-910 (2014).</li>
<li>Klingberg, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Fully+automated+evaluation+of+total+glomerular+number+and+capillary+tuft+size+in+nephritic+kidneys+using+lightsheet+microscopy%5BTitle%5D)+AND+%22Journal+of+the+American+Society+of+Nephrology%22%5BJournal%5D)">Fully automated evaluation of total glomerular number and capillary tuft size in nephritic kidneys using lightsheet microscopy.</a> Journal of the American Society of Nephrology. 28 (2), 452-459 (2017).</li>
<li>Zhao, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Cellular+and+molecular+probing+of+intact+human+organs%5BTitle%5D)+AND+%22Cell%22%5BJournal%5D)">Cellular and molecular probing of intact human organs.</a> Cell. 180 (4), 796-812 (2020).</li>
<li>Susaki, E. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Versatile+whole-organ%2Fbody+staining+and+imaging+based+on+electrolyte-gel+properties+of+biological+tissues%5BTitle%5D)+AND+%22Nature+Communications%22%5BJournal%5D)">Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues.</a> Nature Communications. 11 (1), 1-22 (2020).</li>
</ol>

The authors have nothing to disclose.

The present protocol allowed whole-kidney 3D imaging of various structures such as sympathetic nerves, collecting ducts, arteries, proximal tubules, and glomeruli9,10,11. This staining method offered macroscopic observation and led to new biological discoveries, by visualizing the alteration in renal sympathetic nerves after ischemia-reperfusion injury9,10 and glomerulom...

The kidney is composed of various cell populations. Although conventional pathology gives us much information about the kidney microenvironment, three-dimensional (3D) imaging is needed to precisely understand the intercellular crosstalk during kidney disease progression. In the past, a huge number of serial sectioning and image reconstruction needed to be performed for the whole-organ 3D imaging1. However, this method required too much effort and had problems in terms of reproducibility.
Optical clearing is a good strategy to overcome this hurdle2,3. Tissue opacity is mainly due to light scattering and absorption because each organ consists of various substances, including water, protein, and lipids. Thus, the basic strategy of tissue clearing is replacing water and lipids in tissues with refractive index (RI) matching reagents that have the same optical properties as proteins4. In order to observe a transparent specimen, a light sheet fluorescent microscopy is useful5. Light sheets illuminate the transparent specimen from the side, and excitation signals are acquired through the objective lens located in a vertical position6. This microscopy obtains cross-section information in a single sweep, which is different from the confocal or multiphoton fluorescent microscopy. Thus, it can quickly acquire z-stack images with a low level of photobleaching.
Clear, Unobstructed Brain/Body Imaging Cocktails and Computational Analysis (CUBIC) is one of the tissue clearing methods which enables whole-organ imaging by light sheet fluorescent microscopy2,7,8. CUBIC and whole-mount immunofluorescent staining are optimized in the present study to visualize mouse kidney 3D structures9,10,11. Using this whole-mount staining method, the alteration in renal sympathetic nerves is visualized after ischemia-reperfusion injury9,10 and glomerulomegaly in the early stage of diabetic kidney disease11, as well as blood vessels, proximal tubules, and collecting ducts in a whole kidney9.

<table><tbody><tr><td>14 mL Round Bottom High Clarity PP Test Tube</td><td>Falcon</td><td>352059</td><td>Tissue clearing, staining, wash</td></tr><tr><td>2,3-dimethyl-1-phenyl-5-pyrazolone/antipyrine</td><td>Tokyo Chemical Industry</td><td>D1876</td><td>CUBIC-R+</td></tr><tr><td>37%-Formaldehyde Solution</td><td>Nacalai Tesque</td><td>16223-55</td><td>Post fixation</td></tr><tr><td>4%-Paraformaldehyde Phosphate Buffer Solution</td><td>Nacalai Tesque</td><td>09154-85</td><td>Kidney fixation</td></tr><tr><td>Alexa Flour 555-conjugated donkey anti-sheep IgG antibody</td><td>Invitrogen</td><td>A-21436</td><td>Secondary antibody (1:100)</td></tr><tr><td>Alexa Flour 647-conjugated donkey anti-rabbit IgG antibody</td><td>Invitrogen</td><td>A-31573</td><td>Secondary antibody (1:200)</td></tr><tr><td>Anti-aquaporin 2 (AQP2) antibody</td><td>Abcam</td><td>ab199975</td><td>Primary antibody (1:100)</td></tr><tr><td>Anti-podocin antibody</td><td>Sigma-Aldrich</td><td>P0372</td><td>Primary antibody (1:100)</td></tr><tr><td>Anti-sodium glucose cotransporter 2 (SGLT2) antibody</td><td>Abcam</td><td>ab85626</td><td>Primary antibody (1:100)</td></tr><tr><td>Anti-tyrosine hydroxylase (TH) antibody</td><td>Abcam</td><td>ab113</td><td>Primary antibody (1:100)</td></tr><tr><td>Anti-&amp;alpha;-smooth muscle actin (&amp;alpha;-SMA) antibody</td><td>Abcam</td><td>ab5694</td><td>Primary antibody (1:200)</td></tr><tr><td>Blocker Casein in PBS</td><td>Thermo Fisher Scientific</td><td>37528</td><td>Staining buffer</td></tr><tr><td>Butorphanol Tartrate</td><td>Meiji</td><td>005526</td><td>Anesthetic</td></tr><tr><td>C57BL/6NJcl</td><td>Nippon Bio-Supp.Center</td><td>N/A</td><td>Mouse strain</td></tr><tr><td>Imaris</td><td>Bitplane</td><td>N/A</td><td>Imaging analysis software</td></tr><tr><td>Macro-zoom microscope</td><td>OLYMPUS</td><td>MVX10</td><td>The observation unit of the custom-built microscope</td></tr><tr><td>Medetomidine Hydrochloride</td><td>Kyoritsu-Seiyaku</td><td>008656</td><td>Anesthetic</td></tr><tr><td>Midazolam</td><td>SANDOZ</td><td>27803229</td><td>Anesthetic</td></tr><tr><td>Mineral oil</td><td>Sigma-Aldrich</td><td>M8410</td><td>Immersion oil</td></tr><tr><td>N-buthyldiethanolamine</td><td>Tokyo Chemical Industry</td><td>B0725</td><td>CUBIC-L, CUBIC-R+</td></tr><tr><td>Nicotinamide</td><td>Tokyo Chemical Industry</td><td>N0078</td><td>CUBIC-R+</td></tr><tr><td>Polyethylene glycol mono-p-isooctylphenyl ether/Triton X-100</td><td>Nacalai Tesque</td><td>12967-45</td><td>CUBIC-L, PBST</td></tr><tr><td>Silicon oil HIVAC-F4</td><td>Shin-Etsu Chemical</td><td>50449832</td><td>Immersion oil</td></tr><tr><td>Sodium azide</td><td>Wako</td><td>195-11092</td><td>Staining buffer</td></tr></tbody></table>

whole-kidney three-dimensional staining with cubic

Although conventional pathology provided numerous information about kidney microstructure, it was difficult to know the precise structure of blood vessels, proximal tubules, collecting ducts, glomeruli, and sympathetic nerves in the kidney due to the lack of three-dimensional (3D) information. Optical clearing is a good strategy to overcome this big hurdle. Multiple cells in a whole organ can be analyzed at single-cell resolution by combining tissue clearing and 3D imaging technique. However, cell labeling methods for whole-organ imaging remain underdeveloped. In particular, whole-mount organ staining is challenging because of the difficulty in antibody penetration. The present protocol developed a whole-mount mouse kidney staining for 3D imaging with the CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis) tissue clearing method. The protocol has enabled visualizing renal sympathetic denervation after ischemia-reperfusion injury and glomerulomegaly in the early stage of diabetic kidney disease from a comprehensive viewpoint. Thus, this technique can lead to new discoveries in kidney research by providing a macroscopic perspective.

Using this staining method, sympathetic nerves [anti-tyrosine hydroxylase (TH) antibody] and arteries [anti-&#945;-smooth muscle actin (&#945;SMA) antibody] in a whole kidney (Figure 4A,B and Video 1) were visualized9. Abnormal renal sympathetic nerves were also visualized after ischemia/reperfusion injury (IRI)9,10 (Figure 4C). Moreover, visualiz...

Watch this Scientific Journal Video about Whole-Kidney Three-Dimensional Staining with CUBIC at JoVE.com

Whole-Kidney Three-Dimensional Staining with CUBIC

The present protocol describes a tissue clearing method and whole-mount immunofluorescent staining for three-dimensional (3D) kidney imaging. This technique can offer macroscopic perspectives in kidney pathology, leading to new biological discoveries.

Although conventional pathology provided numerous information about kidney microstructure, it was difficult to know the precise structure of blood ...

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3.8K Views.  The University of Tokyo. The present protocol describes a tissue clearing method and whole-mount immunofluorescent staining for three-dimensional (3D) kidney imaging. This technique can offer macroscopic perspectives in kidney pathology, leading to new biological discoveries.

Video: Whole-Kidney Three-Dimensional Staining with CUBIC

Quantifying Glomerular Permeability of Fluorescent Macromolecules Using 2-Photon Microscopy in Munich Wistar Rats

Kidney diseases involving urinary loss of large essential macromolecules, such as serum albumin, have long been thought to be caused by alterations in the permeability barrier comprised of podocytes, vascular endothelial cells, and a basement membrane working in unison. Data from our laboratory using intravital 2-photon microscopy revealed a more permeable glomerular filtration barrier (GFB) than previously thought under physiologic conditions, with retrieval of filtered albumin occurring in an early subset of cells called proximal tubule cells (PTC)1,2,3.
Previous techniques used to study renal filtration and establishing the characteristic of the filtration barrier involved micropuncture of the lumen of these early tubular segments with sampling of the fluid content and analysis4. These studies determined albumin concentration in the luminal fluid to be virtually non-existent; corresponding closely to what is normally detected in the urine. However, characterization of dextran polymers with defined sizes by this technique revealed those of a size similar to serum albumin had higher levels in the tubular lumen and urine; suggesting increased permeability5.
Herein is a detailed outline of the technique used to directly visualize and quantify glomerular fluorescent albumin permeability in vivo. This method allows for detection of filtered albumin across the filtration barrier into Bowman's space (the initial chamber of urinary filtration); and also allows quantification of albumin reabsorption by proximal tubules and visualization of subsequent albumin transcytosis6. The absence of fluorescent albumin along later tubular segments en route to the bladder highlights the efficiency of the retrieval pathway in the earlier proximal tubule segments. Moreover, when this technique was applied to determine permeability of dextrans having a similar size to albumin virtually identical permeability values were reported2. These observations directly support the need to expand the focus of many proteinuric renal diseases to included alterations in proximal tubule cell reclamation.

A technique utilizing high resolution intavital 2-photon microscopy to directly visualize and quantify gloemrular filtration in surface glomeruli. This method allows for direct determination of permeability characteristics of macromolecules in both normal and diseased states.

Kidney  diseases involving urinary loss of large essential macromolecules, such as  serum albumin, have long been thought to be caused by alterations in ...

Three-Dimensional Imaging of Tumor-Bearing Tissue Using the Iterative Bleaching Extends Multiplexity Approach

The spatial heterogeneity of the tumor microenvironment (TME) is a critical determinant of therapeutic response, particularly for immune-oncology agents, where success depends on the distribution of specific immune cell subpopulations. Over the past decade, multiple sophisticated technologies have been introduced to achieve detailed resolution of the TME using two-dimensional sections from either formalin-fixed, paraffin-embedded (FFPE) or fixed-frozen tissues. While these thin sections are easier to procure and analyze, they lack the three-dimensional architecture needed to reliably and comprehensively characterize a tumor. To address this limitation, a tissue mounting and imaging technique was developed to enable the three-dimensional analysis of tumor lesions in their native in vivo state. This protocol outlines the procurement of human tumor tissue, the mounting of samples on custom-printed platforms, and staining procedures for post-fixation samples. The multiplexed immunofluorescence technique, IBEX (Iterative Bleaching Extends Multiplexity), was adapted to characterize the three-dimensional TME with up to 15 markers for tumor, immune, and stromal cells using commercially available antibodies. Imaging depths of up to 100 &#181;m were achieved using an inverted white-light laser confocal microscope with a custom-printed imaging adaptor and commercial glass-bottom dishes to ensure optimal tissue orientation. This protocol highlights the potential of the IBEX method to expand multiplexed immunofluorescence studies, providing a more comprehensive understanding of TME composition.

This article describes a protocol for multiplex immunofluorescence optimized to characterize the three-dimensional architecture of peritoneal metastases.

The spatial heterogeneity of the tumor microenvironment (TME) is a critical determinant of therapeutic response, particularly for immune-oncology agents, ...

Cancer Research

3D Imaging of Soft-Tissue Samples using an X-ray Specific Staining Method and Nanoscopic Computed Tomography

We demonstrate a laboratory-based method combining X-ray microCT and nanoCT with a specific X-ray stain, which targets the cell cytoplasm. The described protocol is easy to apply, fast and suitable for larger soft-tissue samples. The presented methodology enables the characterization of crucial tissue structures in three dimensions and is demonstrated on a whole mouse kidney. The multiscale approach allows to image the entire mouse kidney and supports the selection of further volumes of interest, which are acquired with higher resolutions ranging into the nanometer range. Thereby, soft-tissue morphology with a similar detail level as the corresponding histological light microscopy images is reproduced. Deeper insights into the 3D configuration of tissue structures are achieved without impeding further investigations through histological methods.

A protocol for 3D visualization of microscopic tissue structures by using an X-ray specific staining method designed for X-ray computed tomography is presented.

We demonstrate a laboratory-based method combining X-ray microCT and nanoCT with a specific X-ray stain, which targets the cell cytoplasm. The described ...

Bioengineering

Optical Clearing and Imaging of Immunolabeled Kidney Tissue

Optical clearing techniques render tissue transparent by equilibrating the refractive index throughout a sample for subsequent three-dimensional (3-D) imaging. They have received great attention in all research areas for the potential to analyze microscopic multicellular structures that extend over macroscopic distances. Given that kidney tubules, vasculature, nerves, and glomeruli extend in many directions, which have been only partially captured by traditional two-dimensional techniques so far, tissue clearing also opened up many new areas of kidney research. The list of optical clearing methods is rapidly growing, but it remains difficult for beginners in this field to choose the best method for a given research question. Provided here is a simple method that combines antibody labeling of thick mouse kidney slices; optical clearing with cheap, non-toxic and ready-to-use chemical ethyl cinnamate; and confocal imaging. This protocol describes how to perfuse kidneys and use an antigen-retrieval step to increase antibody- binding without requiring specialized equipment. Its application is presented in imaging different multicellular structures within the kidney, and how to troubleshoot poor antibody penetration into tissue is addressed. We also discuss the potential difficulties of imaging endogenous fluorophores and acquiring very large samples and how to overcome them. This simple protocol provides an easy-to-setup and comprehensive tool to study tissue in three dimensions.

The combination of antibody labeling, optical clearing, and advanced light microscopy allows three-dimensional analysis of complete structures or organs. Described here is a simple method to combine immunolabeling of thick kidney slices, optical clearing with ethyl cinnamate, and confocal imaging that enables visualization and quantification of three-dimensional kidney structures.

Optical clearing techniques render tissue transparent by equilibrating the refractive index throughout a sample for subsequent three-dimensional (3-D) ...

Analysis of Nephron Composition and Function in the Adult Zebrafish Kidney

The zebrafish model has emerged as a relevant system to study kidney development, regeneration and disease. Both the embryonic and adult zebrafish kidneys are composed of functional units known as nephrons, which are highly conserved with other vertebrates, including mammals. Research in zebrafish has recently demonstrated that two distinctive phenomena transpire after adult nephrons incur damage: first, there is robust regeneration within existing nephrons that replaces the destroyed tubule epithelial cells; second, entirely new nephrons are produced from renal progenitors in a process known as neonephrogenesis. In contrast, humans and other mammals seem to have only a limited ability for nephron epithelial regeneration. To date, the mechanisms responsible for these kidney regeneration phenomena remain poorly understood. Since adult zebrafish kidneys undergo both nephron epithelial regeneration and neonephrogenesis, they provide an outstanding experimental paradigm to study these events. Further, there is a wide range of genetic and pharmacological tools available in the zebrafish model that can be used to delineate the cellular and molecular mechanisms that regulate renal regeneration. One essential aspect of such research is the evaluation of nephron structure and function. This protocol describes a set of labeling techniques that can be used to gauge renal composition and test nephron functionality in the adult zebrafish kidney. Thus, these methods are widely applicable to the future phenotypic characterization of adult zebrafish kidney injury paradigms, which include but are not limited to, nephrotoxicant exposure regimes or genetic methods of targeted cell death such as the nitroreductase mediated cell ablation technique. Further, these methods could be used to study genetic perturbations in adult kidney formation and could also be applied to assess renal status during chronic disease modeling.

The zebrafish adult kidney is an excellent system for renal regeneration and disease studies. An essential aspect of such research is the assessment of nephron structure and function. This protocol describes several methodologies that can be implemented to assess nephron tubule composition and to evaluate renal reabsorption.

The zebrafish model has emerged as a relevant system to study kidney development, regeneration and disease. Both the embryonic and adult zebrafish kidneys ...

Biology

Using 2-Photon Microscopy to Quantify the Effects of Chronic Unilateral Ureteral Obstruction on Glomerular Processes

Applying novel microscopy methods to suitable animal disease models to explore the dynamic physiology of the kidney remains a challenge. Rats with surface glomeruli provide a unique opportunity to investigate physiological and pathophysiological processes using intravital 2-photon microscopy. Quantification of glomerular capillary blood flow and vasoconstriction and dilatation in response to drugs, permeability, and inflammation are just some of the processes that can be studied. In addition, transgenic rats, i.e., podocytes labeled with fluorescent dyes and other molecular biomarker approaches, provide increased resolution to directly monitor and quantify protein-protein interactions and the effects of specific molecular alterations.
In mice, which lack surface glomeruli after four weeks of age, unilateral ureteral obstruction (UUO) for several weeks has been used to induce surface glomeruli. As this induction model does not allow for baseline studies, we quantified the effects of UUO on glomerular processes in the UUO model in Munich Wistar Fr&#246;mter (MWF) rats, which have surface glomeruli under physiologic conditions. The UUO model for five weeks or more induced significant alterations to gross renal morphology, the peritubular and glomerular microvasculature, as well as the structure and function of tubular epithelia. Glomerular and peritubular red blood cell (RBC) flow decreased significantly (p &#60; 0.01), probably due to the significant increase in the adherence of white blood cells (WBCs) within glomerular and peritubular capillaries. The glomerular sieving coefficient of albumin increased from 0.015 &#177; 0.002 in untreated MWFs to 0.045 &#177; 0.05 in 5-week-old UUO MWF rats. Twelve weeks of UUO resulted in further increases in surface glomerular density and glomerular sieving coefficient (GSC) for albumin. Fluorescent albumin filtered across the glomeruli was not reabsorbed by the proximal tubules. These data suggest that using UUO to induce surface glomeruli limits the ability to study and interpret normal glomerular processes and disease alterations.

Here, we present a protocol using 2-photon microscopy in Munich Wistar Fromter rats with surface glomeruli to quantifythe effects of prolonged ureteral obstruction on glomerular dynamics and function.

Applying novel microscopy methods to suitable animal disease models to explore the dynamic physiology of the kidney remains a challenge. Rats with surface ...

Staining and High-Resolution Imaging of Three-Dimensional Organoid and Spheroid Models

In vitro three-dimensional (3D) cell culture models, such as organoids and spheroids, are valuable tools for many applications including development and disease modeling, drug discovery, and regenerative medicine. To fully exploit these models, it is crucial to study them at cellular and subcellular levels. However, characterizing such in vitro 3D cell culture models can be technically challenging and requires specific expertise to perform effective analyses. Here, this paper provides detailed, robust, and complementary protocols to perform staining and subcellular resolution imaging of fixed in vitro 3D cell culture models ranging from 100 &#181;m to several millimeters. These protocols are applicable to a wide variety of organoids and spheroids that differ in their cell-of-origin, morphology, and culture conditions. From 3D structure harvesting to image analysis, these protocols can be completed within 4-5 days. Briefly, 3D structures are collected, fixed, and can then be processed either through paraffin-embedding and histological/immunohistochemical staining, or directly immunolabeled and prepared for optical clearing and 3D reconstruction (200 &#181;m depth) by confocal microscopy.

Here, we provide detailed, robust, and complementary protocols to perform staining and subcellular resolution imaging of fixed three-dimensional cell culture models ranging from 100 &#181;m to several millimeters, thus enabling the visualization of their morphology, cell-type composition, and interactions.

In vitro three-dimensional (3D) cell culture models, such as organoids and spheroids, are valuable tools for many applications including development and ...

Identification of the Source of Secreted Proteins in the Kidney by Brefeldin A Injection

Chronic kidney disease (CKD) is one of the top ten leading causes of death in the USA. Acute kidney injury (AKI), while often recoverable, predisposes patients to CKD later in life. Kidney epithelial cells have been identified as key signaling nodes in both AKI and CKD, whereby the cells can determine the course of the disease through the secretion of cytokines and other proteins. In CKD especially, several lines of evidence have demonstrated that maladaptively repaired tubular cells drive disease progression through the secretion of transforming growth factor-beta (TGF-&#946;), connective tissue growth factor (CTGF), and other profibrotic cytokines. However, identifying the source and the relative number of secreted proteins from different cell types in vivo remains challenging.
This paper describes a technique using brefeldin A (BFA) to prevent the secretion of cytokines, enabling the staining of cytokines in kidney tissue using standard immunofluorescent techniques. BFA inhibits endoplasmic reticulum (ER)-to-Golgi apparatus transport, which is necessary for the secretion of cytokines and other proteins. Injection of BFA 6 h before sacrifice leads to a build-up of TGF-&#946;, PDGF, and CTGF inside the proximal tubule cells (PTCs) in a mouse cisplatin model of AKI and TGF-&#946; in&#160;a mouse aristolochic acid (AA) model of CKD. Analysis revealed that BFA + cisplatin or BFA + AA increased TGF-&#946;-positive signal significantly compared to BFA + saline, cisplatin, or AA alone. These data suggest that BFA can be used to identify the cell type producing specific cytokines and quantify the relative amounts and/or different types of cytokines produced.

Identifying the cell type responsible for secreting cytokines is necessary to understand the pathobiology of kidney disease. Here, we describe a method to quantitatively stain kidney tissue for cytokines produced by kidney epithelial or interstitial cells using brefeldin A, a secretion inhibitor, and cell-type-specific markers.

Chronic kidney disease (CKD) is one of the top ten leading causes of death in the USA. Acute kidney injury (AKI), while often recoverable, predisposes ...

Fluorescent Labeling of Glomeruli in Cleared Mouse Kidneys for Microscopy

An Efficient and Fast Method for Labeling and Analyzing Mouse Glomeruli

The glomeruli are fundamental units in the kidney; hence, studying the glomeruli is pivotal for understanding renal function and pathology. Biological imaging provides intuitive information; thus, it is of great significance to label and observe the glomeruli. However, the glomeruli observation methods currently in use require complicated operations, and the results may lose label details or three-dimensional (3D) information. The clear, unobstructed brain imaging cocktails and computational analysis (CUBIC) tissue clearing technology has been widely used in renal research, allowing for more accurate detection and deeper detection depth. We found that mouse glomeruli can be rapidly and effectively labeled by tail vein injection of medium molecular weight FITC-Dextran followed by the CUBIC clearing method. The cleared mouse kidney could be scanned by a light-sheet microscope (or a confocal microscope when sliced) to obtain three-dimensional image stacks of all the glomeruli in the entire kidney. Processed with appropriate software, the glomeruli signals could be easily digitized and further analyzed to measure the number, volume, and frequency of the glomeruli.

Author Spotlight: Aiding Research in Kidney Biology by Labeling Glomeruli in Cleared Tissues 

This study presents an easy-to-use, complete, and simple set of methods to label and analyze glomeruli from CUBIC-cleared mouse kidneys. Data such as glomerulus number and volume can be obtained easily and reliably using fluorescein isothiocyanate (FITC)-Dextran, light sheet fluorescence microscopy (LSFM), or common confocal microscopy and software such as Imaris.

The glomeruli are fundamental units in the kidney; hence, studying the glomeruli is pivotal for understanding renal function and pathology. Biological ...

Kidney Flat Mount Preparation: A Procedure to Dissect and Prepare a Flat Mount for Microscopic Analysis of Adult Zebrafish Kidney

Source: McCampbell, K. K. et al. <a href="https://www.jove.com/video/51644" target="_blank">Analysis of Nephron Composition and Function in the Adult Zebrafish Kidney.</a>&#160;J. Vis. Exp. (2014)
This video demonstrates the dissection and preparation of a flat mount of the adult zebrafish kidney. The prepared flat mount can be visualized under the microscope for specimen analysis.