This protocol describes methods for sectioning, staining, and imaging free-floating tissue sections of the mouse brain, followed by a detailed description of the analysis of astrocyte territory volume and astrocyte territory overlap or tiling.
Astrocytes possess an astounding degree of morphological complexity that enables them to interact with nearly every type of cell and structure within the brain. Through these interactions, astrocytes actively regulate many critical brain functions, including synapse formation, neurotransmission, and ion homeostasis. In the rodent brain, astrocytes grow in size and complexity during the first three postnatal weeks and establish distinct, non-overlapping territories to tile the brain. This protocol provides an established method for analyzing astrocyte territory volume and astrocyte tiling using free-floating tissue sections from the mouse brain. First, this protocol describes the steps for tissue collection, cryosectioning, and immunostaining of free-floating tissue sections. Second, this protocol describes image acquisition and analysis of astrocyte territory volume and territory overlap volume, using commercially available image analysis software. Lastly, this manuscript discusses the advantages, important considerations, common pitfalls, and limitations of these methods. This protocol requires brain tissue with sparse or mosaic fluorescent labeling of astrocytes, and is designed to be used with common lab equipment, confocal microscopy, and commercially available image analysis software.
Astrocytes are elaborately branched cells that perform many important functions in the brain1. In the mouse cortex, radial glial stem cells give rise to astrocytes during the late embryonic and early postnatal stages2. During the first three postnatal weeks, astrocytes grow in size and complexity, developing thousands of fine branches that directly interact with synapses1. Concurrently, astrocytes interact with neighboring astrocytes to establish discrete, non-overlapping territories to tile the brain3, while maintaining communication via gap junction channels4. Astrocyte morphology and organization are disrupted in many disease states following insult or injury5, indicating the importance of these processes for proper brain function. Analysis of astrocyte morphological properties during normal development, aging, and disease can provide valuable insights into astrocyte biology and physiology. Furthermore, analysis of astrocyte morphology following genetic manipulation is a valuable tool for discerning the cellular and molecular mechanisms that govern the establishment and maintenance of astrocyte morphological complexity.
Analysis of astrocyte morphology in the mouse brain is complicated by both astrocyte branching complexity and astrocyte tiling. Antibody staining using the intermediate filament glial fibrillary acidic protein (GFAP) as an astrocyte-specific marker captures only the major branches, and vastly underestimates astrocyte morphological complexity1. Other cell-specific markers such as glutamate transporter 1 (GLT-1; slc1a2), glutamine synthetase, or S100β do a better job of labeling astrocyte branches6, but introduce a new problem. Astrocyte territories are largely non-overlapping, but a small degree of overlap exists at the peripheral edges. Because of the complexity of branching, when neighboring astrocytes are labeled the same color, it is impossible to distinguish where one astrocyte ends and the other begins. Sparse or mosaic labeling of astrocytes with endogenous fluorescent proteins solves both problems: the fluorescent marker fills the cell to capture all of the branches and allows for imaging of individual astrocytes that can be distinguished from their neighbors. Several different strategies have been used to achieve sparse fluorescent labeling of astrocytes, with or without genetic manipulation, including viral injection, plasmid electroporation, or transgenic mouse lines. Details on the execution of these strategies are described in previously published studies and protocols1,7,8,9,10,11,12,13.
This article describes a method for measuring astrocyte territory volume from mouse brains with fluorescent labeling in a sparse population of astrocytes (Figure 1). Because the average diameter of an astrocyte in the mouse cortex is approximately 60 µm, 100 µm thick sections are used to improve the efficiency in capturing individual astrocytes in their entirety. Immunostaining is not required but is recommended to enhance the endogenous fluorescent signal for confocal imaging and analysis. Immunostaining may also enable better detection of fine astrocyte branches and reduce photobleaching of endogenous proteins during image acquisition. To improve antibody penetration into the thick sections, and to preserve tissue volume from sectioning through imaging, free-floating tissue sections are used. Analysis of astrocyte territory volume is performed using commercially available image analysis software. Additionally, this protocol describes a method for analysis of astrocyte tiling in tissue sections with mosaic labeling, where neighboring astrocytes express different fluorescent labels. This protocol has been used successfully in several recent studies1,8,9 to characterize astrocyte growth during normal brain development, as well as the impact of genetic manipulation on astrocyte development.
All mice were used in accordance with the Institutional Animal Care and Use Committee (IACUC) at the University of North Carolina at Chapel Hill and the Division of Comparative Medicine (IACUC protocol number 21-116.0). Mice of both sexes at postnatal day 21 (P21) were used for these experiments. CD1 mice were obtained commercially (Table of Materials), and MADM9 WT:WT and MADM9 WT:KO mice were described previously9.
NOTE: This protocol requires brains with fluorescent protein expression in a sparse population of astrocytes. Fluorescent protein expression can be introduced genetically, virally, or by electroporation. Details of methods to sparsely label astrocytes are described in previously published studies and protocols1,7,8,9,10,11,12,13.
1. Tissue collection and preparation
CAUTION: Paraformaldehyde (PFA) is a hazardous chemical. Perform all steps with PFA in a chemical fume hood.
2. Cyrosectioning
NOTE: This sectioning method is intended to work with many different commercially available cryostats. With the cryostat used here (Table of Materials), the optimal specimen head cutting temperature is -23 °C, with an ambient chamber temperature between -23 °C and -25 °C.
CAUTION: The cryostat blade is extremely sharp. Use caution while manipulating the blade and operating the cryostat.
3. Immunostaining
NOTE: Perform all washes and incubations on an orbital platform shaker set to approximately 100 rpm. All steps are performed at room temperature, except the primary antibody incubation, which is performed at 4 °C. Prepare mounting media ahead of time by combining the ingredients in a 50 mL tube and mixing on a nutator overnight. Protect from light and store at 4 °C for up to 2 months. If the endogenous fluorescent signal is sufficient for imaging and analysis without the need for immunostaining, steps 3.1-3.9 can be skipped. If skipping immunostaining, perform three 10 min washes in TBS and proceed to step 3.10.
4. Confocal imaging
NOTE: This protocol gives general image acquisition guidelines that are widely applicable to different confocal microscopes, rather than specific details for a particular confocal and software interface.
5. Image analysis
NOTE: This protocol describes the steps for performing image analysis using commercially available image analysis software (i.e., Imaris; see Table of Materials). Other versions of this software may be used with minor modifications to the workflow. This protocol also requires MATLAB to run the Convex Hull XTension file (Supplemental File).
Figure 1 presents a schematic outline of the major steps and workflow for this protocol. Figure 2 shows screenshots of key steps using the image analysis software to generate a surface, generate spots close to the surface, and generate a convex hull. Figure 3 demonstrates the application of this technique to determine astrocyte territory overlap/tiling. In Figure 4, representative results from a previously published manuscript9 demonstrate the application of this protocol. In Figure 4A and Figure 4B, knockdown of the astrocyte-enriched cell adhesion molecule hepaCAM significantly reduces astrocyte territory volume. In Figure 4C and Figure 4D, Mosaic Analysis with Double Markers (MADM) was used to introduce sparse mosaic labeling and concurrent genetic modification into the mouse cortex. With MADM, mice were generated where wild-type astrocytes express a red fluorescent protein (RFP) and Hepacam knockout astrocytes express a green fluorescent protein (GFP). Using the protocol described above, the percentage of territory overlap between neighboring RFP and GFP astrocyte pairs (WT:KO) was calculated. As a control, this was compared to neighboring RFP and GFP astrocyte pairs in mice with no genetic modification of Hepacam (WT:WT). WT:KO astrocyte pairs showed a significantly increased percentage of territory overlap volume compared to WT:WT astrocyte pairs. Collectively, these results demonstrate that hepaCAM is required for normal astrocyte territory volume and astrocyte tiling.
Figure 1: Overview of workflow for analyzing astrocyte territory volume. (A) The protocol requires a mouse with sparse or mosaic fluorescent labeling of astrocytes. (B) The mouse is perfused and then the brain is resected, processed, and frozen. (C) The frozen brain is sectioned using a cryostat and (D) the free-floating tissue sections are collected. (E) After sectioning, the floating tissue sections are stained by immunohistochemistry and then (F) mounted onto slides. (G) Astrocytes within the mounted tissue sections are imaged using confocal microscopy. (H) Finally, the imaged cells' territory volumes are quantified using image analysis software. Please click here to view a larger version of this figure.
Figure 2: Key steps in image analysis procedure for astrocyte territory volume. (A) View of cell with region of interest box that excludes other signal in the image from the analysis procedure. (B) An acceptable relative threshold for surface creation (gray) using signal (red). (C) Completed surface with main cell selected (yellow). Other parts of the surface that aren't the cell will be deleted (red). (D) Translucent surface with spots created. (E) Close-up of the translucent surface with spots created to show an acceptable distribution of spots relative to the surface. (F) Final convex hull. Scale bars = 20 µm. Please click here to view a larger version of this figure.
Figure 3: Key steps in astrocyte territory overlap analysis. (A) Representative image of two astrocytes expressing different fluorescent markers, GFP (green) and RFP (magenta). (B) Generation of a convex hull for each astrocyte. (C) View of masked GFP and RFP channels, with original channels removed. (D) Example of thresholding using the "Coloc" tool to create a "Colocalization Result" channel. The "colocalized" signal is shown in gray. (E) View of the two masked channels. (F) A rotated view of the convex hull of the "Colocalization Result" channel (gray) which represents the territory overlap volume. Scale bars = 20 µm. Please click here to view a larger version of this figure.
Figure 4: Successful application of the protocol to measure astrocyte territory volume and astrocyte territory overlap. (A) Astrocytes in the visual cortex of wild-type CD1 mice at postnatal day 21, expressing mCherry-CAAX (cyan) and a control shRNA (shScramble) or an shRNA targeting hepaCAM (shHepacam). The astrocyte territory is outlined in red. (B) Loss of hepaCAM significantly reduces astrocyte territory volume. Data points represent individual mouse averages. Error bars are ± s.e.m. Nested t-test. (C) Neighboring astrocytes in the mouse cortex at postnatal day 21 expressing GFP (green) or RFP (magenta). In MADM9 WT:WT mice, both astrocytes are wild-type. In MADM9 WT:KO mice, the green astrocyte is wild-type and the magenta astrocyte is null for Hepacam. Territory overlap volume is shown in blue. (MADM9 WT:WT genotype: MADM9TG/GT; EMX-CreTg/0; Hepacam+/+. MADM9 WT:KO genotype: MADM9TG/GT; EMX-CreTg/0; Hepacam+/-). (D) Quantification of the percentage of territory volume overlap. Data points represent individual mouse averages. Error bars are ± s.e.m. Nested t-test. Scale bars = 20 µm. The panels in this figure are reprinted from Baldwin et al9 with permission from the publisher. Please click here to view a larger version of this figure.
Supplemental File. Please click here to download this File.
This protocol describes an established method for analyzing astrocyte territory volume and astrocyte tiling in the mouse cortex, detailing all of the major steps beginning with perfusion and ending with image analysis. This protocol requires brains from mice that express fluorescent proteins in a sparse or mosaic population of astrocytes. Outside of this requirement, mice of any age may be used for this protocol, with only minor adjustments to perfusion settings and the volume of freezing media added to the embedding mold. While other methods have been published for analysis of astrocyte branching complexity and volume in brain tissue sections7,11, this protocol has several unique advantages. First, this protocol describes a custom code that can be used to obtain astrocyte territory volume. Astrocyte territory volume is a distinct measurement from astrocyte cell volume, in that it measures the entire space occupied by an astrocyte, regardless of its branching complexity. Furthermore, this protocol describes how to apply the astrocyte territory volume measurement to measure astrocyte territory overlap volume, and therefore astrocyte tiling behavior. Lastly, this protocol provides a detailed discussion of the potential variables that may influence astrocyte territory volume and data collection, including mounting conditions, sample storage conditions, and inclusion and exclusion criteria for imaging and analysis. In addition to these unique features, many aspects of this protocol, including the perfusion, cryosectioning, and immunostaining of free-floating sections, can be broadly applied to staining brain tissue sections of different thicknesses and with different antibody combinations. Below, critical steps, important considerations, troubleshooting, and limitations are discussed in detail.
Sample collection considerations
One very important consideration for experiments designed to investigate astrocyte morphology is maintaining a consistent time of day for sample collection. Growing evidence indicates that astrocyte functional states are linked to circadian rhythm and sleep behaviors14. To remove any variability that may be introduced by samples being collected at different times of day, perfusions should be planned so that all samples for an experiment are collected at roughly the same time of day, within a time range of 2-3 h. For consistent perfusions, the use of a peristaltic pump is highly recommended. The addition of heparin to the TBS is helpful to reduce the formation of blood clots. While this protocol has not been tested with shorter post-fixation times, post-fixation overnight may not be required, and a shorter post-fixation of 4 h may be considered.
Troubleshooting tips for cryosectioning
Freezing brains in the 2:1 Sucrose:OCT freezing medium reduces the amount of OCT in the collection wells after sectioning. When frozen, the freezing medium behaves similarly to OCT itself but is less brittle. When freezing the tissue block to the chuck, be sure to press it flat on the chuck immediately after adding OCT to the chuck. If the tissue block breaks off from the chuck during sectioning, use a razor blade to cut a new flat surface on the bottom and refreeze to the chuck. Giving the chuck sufficient time to cool to the cryostat chamber temperature before adding the OCT and making sure that the chuck is clean and dry will improve adherence. When moving tissue sections with the paintbrush, touch the paintbrush to the corner edge of the section, so that is it touching the OCT and not the tissue itself. With a little bit of moisture, the section will stick to the brush. Gently place the tissue into the sectioning medium by touching the opposite edge of the section to the media and allowing it to be pulled into the medium. If the brush touches the freezing medium, wipe it off on a paper towel within the cryostat. A brush that is too wet will make it difficult to transfer sections to the dish. OCT should dissolve once the tissue section is placed in the sectioning medium. If it doesn't, the cryostat chamber temperature may be too low.
Important considerations for staining and mounting tissue sections
To improve staining quality, prepare TBST fresh before each experiment. Use a high-quality 10% aqueous Triton source (Table of Materials). Choose a serum that matches the species in which the secondary antibody was made (e.g., use goat serum for a goat anti-rabbit secondary). Antibody solutions are centrifuged prior to use, to pellet and remove any precipitated antibody. Take care not to disturb the pellet when transferring antibody solution from the tube to the plate (this may mean pipetting slightly less than 1 mL of antibody solution per well as to not touch the bottom of the tube with the pipette tip). This step helps to reduce background staining. When sections are placed in TBS:dH2O, most will unfold/untangle themselves, but some may remain folded or twisted. When transferring sections to the slide using a brush, use a P200 tip in the other hand to help guide the tissue section to the appropriate spot. Use the brush to gently unfold or untwist sections so that they lay flat. Sections tend to move toward the aspirating pipet as the liquid is removed. Use the P200 tip to keep mobile sections in place while aspirating. Mounting media must be added to the sections immediately after all the excess liquid is removed and before the sections have time to dry. Allowing the sections to dry even for a few minutes will drastically impact the volume of the cells within the section. After adding the mounting media to the slide, use a pipet to remove any visible bubbles. After adding the coverslip, make sure to remove excess mounting media from the sides, as this will interfere with the ability of the nail polish to dry. Allow the nail polish to dry at room temperature. Wait for at least 2 h or until the next day to image the sections, to ensure that the mounting media has enough time to completely penetrate the thick sections.
Imaging complete astrocytes
When imaging astrocytes for territory volume analysis, it is critical that the image captures the entire volume of the astrocyte. Many labeled astrocytes in the tissue section will be incomplete astrocytes. Complete astrocytes will be fully contained within the tissue section. To identify complete astrocytes, begin with a focal point within the middle of the astrocyte. Use the focus knob to move to the top of the astrocyte. When the astrocyte is no longer in focus, other features of the tissue should remain in focus. Repeat this process for the bottom of the astrocyte. Do not image incomplete astrocytes. Because of the thickness of the sections, antibody penetration is not as robust in the middle of the section. Labeling may be stronger around the outer edges of the astrocyte and weaker in the center. This is commonly observed and does not impact territory analysis.
Tips for image analysis
The most important consideration for the image analysis portion of the protocol is to ensure that the convex hull represents only one astrocyte. Follow the inclusion and exclusion criteria each time. Sometimes two astrocytes will have their cell bodies very close to one another. This can be difficult to identify in the 3D view, but is identifiable using the slice view. If there are other fluorescently labeled astrocytes contacting the astrocyte of interest, this can complicate the surface creation process. If a reasonably clear boundary is visible between the two cells (for example, they connect only at one small branch point), the clip tool can be used to make a cut in the surface, and this part of the surface can be deleted. After creating the surface, rotate the cell in 3D view to check for small bits of surface that may be hiding behind the cell, but are not part of the cell. Delete these before proceeding. If the convex hull protrudes drastically to a point outside of the astrocyte territory, there likely is a piece of non-cell surface that was not removed. If the software routinely crashes during surface creation, the surface detail number can be reduced. If it crashes during spots creation, use a region of interest to create spots only near the surface object.
Limitations of the protocol
While there are many uses and advantages to this protocol, there are also several limitations. This protocol requires mice that already express fluorescent proteins in a sparse population of astrocytes, but does not describe the methods for introducing the expression of fluorescent proteins in astrocytes. The imaging and analysis pipelines are time-consuming and are not well-suited for high-throughput analysis. Furthermore, they are geared specifically toward measuring astrocyte territory volume and tiling, rather than defining the detailed morphological features of individual astrocytes. Others may find it useful to combine approaches and strategies of this protocol with recently published protocols that detail methods for measuring astrocyte morphological complexity7,11. Lastly, the commercial software platforms used in this protocol (i.e., Imaris and MATLAB) are expensive and require a license to use. While large institutions often purchase licenses for these software platforms, this could be cost-prohibitive for smaller institutions and individual labs. Advancements in microscopy, open-source image analysis software, and machine learning algorithms may help make this protocol widely accessible to all labs, and may also improve the efficiency of image acquisition and analysis.
The authors have nothing to disclose.
Microscopy was performed at the UNC Neuroscience Microscopy Core (RRID:SCR_019060), supported in part by funding from the NIH-NINDS Neuroscience Center Support Grant P30 NS045892 and the NIH-NICHD Intellectual and Developmental Disabilities Research Center Support Grant U54 HD079124. Figure 1 was created with BioRender.com. The images and data in Figure 4 are reprinted from a previous publication9 with permission from the publisher.
#5 forceps | Roboz | RS-5045 | |
1 mL TB Syringe | Becton Dickinson (BD) | 309623 | |
10x TBS (tris-buffered saline) | 30 g Tris, 80 g NaCl, 2 g KCl, HCl to pH 7.4, dH2O to 1 L; store at room temperature (RT) | ||
12-well plate | Genesee Scientific | 25-106MP | |
1x TBS | 100 mL 10x TBS + 900 mL dH2O; store at RT | ||
1x TBS + Heparin | 28.2 mg Heparin + 250 mL 1x TBS; store at 4 °C | ||
24-well plate | Genesee Scientific | 25-107MP | |
30% Sucrose in TBS | 15 g sucrose, 1x TBS to 50 mL; store at 4 °C | ||
4% PFA (paraformaldehyde) in TBS | 40 g PFA, 4-6 NaOH pellets, 100 mL 10x TBS, dH2O to 1 L; store at 4 °C | ||
Avertin | 0.3125 g tri-bromoethanol, 0.625 mL methylbutanol, dH2O to 25 mL; store at 4 °C; discard 2 weeks after making | ||
Blocking and antibody buffer | 10% goat serum in TBST; store at 4 °C | ||
CD1 mice | Charles River | 022 | |
Collection vial for brains | Fisher Scientific | 03-337-20 | |
Confocal acquisition software | Olympous | FV31S-SW | |
Confocal microscope | Olympus | FV3000RS | |
Coverslips | Fisher Scientific | 12544E | |
Cryostat | Thermo Scientific | CryoStar NX50 | |
Cryostat blade | Thermo Scientific | 3052835 | |
DAPI | Invitrogen | D1306 | |
Embedding mold | Polysciences | 18646A-1 | |
Freezing Medium | 2:1 30% sucrose:OCT; store at RT | ||
GFP antibody | Aves Labs | GFP1010 | |
Glycerol | Thermo Scientific | 158920010 | |
Goat anti-chicken 488 | Invitrogen | A-11039 | |
Goat anti-rabbit 594 | Invitrogen | A11037 | |
Goat Serum | Gibco | 16210064 | |
Heparin | Sigma-Aldrich | H3149 | |
Hydrochloric acid | Sigma-Aldrich | 258148 | |
Imaris | Bitplane | N/A | Version 9.8.0 |
MATLAB | MathWorks | N/A | |
Metal lunch tin | AQUARIUS | N/A | From Amazon, "DIY Large Fun Box" |
Methylbutanol | Sigma-Aldrich | 152463 | |
Micro Dissecting Scissors | Roboz | RS-5921 | |
Mouting medium | 20mM Tris pH8.0, 90% Glycerol, 0.5% N-propyl gallate ; store at 4 °C; good for up to 2 months | ||
Nailpolish | VWR | 100491-940 | |
N-propyl gallate | Sigma-Aldrich | 02370-100G | |
O.C.T. | Fisher Scientific | 23-730-571 | |
Oil | Olympus | IMMOIL-F30CC | Specific to microscope/objective |
Operating Scissors 6" | Roboz | RS-6820 | |
Orbital platform shaker | Fisher Scientific | 88861043 | Minimum speed needed: 25 rpm |
Paintbrush | Bogrinuo | N/A | From Amazon, "Detail Paint Brushes – Miniature Brushes" |
Paraformaldehyde | Sigma-Aldrich | P6148 | |
Pasteur pipet (5.75") | VWR | 14672-608 | |
Pasteur pipet (9") | VWR | 14672-380 | |
Potassium chloride | Sigma-Aldrich | P9541-500G | |
Razor blade | Fisher Scientific | 12-640 | |
RFP antibody | Rockland | 600-401-379 | |
Sectioning medium | 1:1 glycerol:1x TBS; store at RT | ||
Slides | VWR | 48311-703 | |
Sodium chrloide | Fisher Scientific | BP358-212 | |
Sodium hydroxide | Sigma-Aldrich | S5881 | |
Sucrose | Sigma-Aldrich | S0389 | |
TBST (TBS + Triton X-100) | 0.2% Triton in 1x TBS; store at RT | ||
Transfer Pipet | VWR | 414004-002 | |
Tri-bromoethanol | Sigma-Aldrich | T48402 | |
Tris(hydroxymethyl)aminomethane | Thermo Scientific | 424570025 | |
Triton X-100 | Sigma-Aldrich | 93443 | |
Triton X-100 (high-quality) | Fisher Scientific | 50-489-120 | |
XTSpotsConvexHull | N/A | N/A | custom XTension provide as supplementary material |
Buffers and Solutions | |||
10x TBS | xx mM Tris, xx mM NaCl, xx mM KCl, pH 7.4 | ||
1x TBS | |||
1x TBS + Heparin | add xx mg Heparin to xx mL of 1x TBS | ||
4% PFA | |||
30% Sucrose in TBS | |||
Freezing Medium | |||
Sectioning medium | |||
TBST | 0.2% Triton in 1x TBS | ||
Blocking and antibody buffer | 10% goat serum in 1x TBST | ||
Mouting medium |