Stefano Fumagalli is a fellow of the Monzino Foundation.

1. Immunofluorescence
The following protocol is performed on coronal brain cryosections obtained from transcardially perfused mice (20 ml of PBS, 0.1 mol/liter, pH 7.4, followed by 50 ml of chilled paraformaldehyde 4% in PBS). After perfusion, brains are carefully removed and transferred to 30% sucrose in PBS at 4 &#176;C overnight for cryoprotection. The brains are then rapidly frozen by immersion in isopentane at - 45 &#176;C for 3 min before being sealed into vials and stored at -70 &#176;C until use. Coronal brain cryosections (20 &#956;m) are cut serially and subjected to immunofluorescence protocol 11, 6.
Bring all reagents and samples to room temperature before use. Please note that the presented working dilutions of antibodies and serum resulted from trials made in order to obtain the best performance. When different antibodies and serum are used, the protocol needs to be validated.
Note that because both anti-CD11b and anti-CD68 primary antibodies are made in rat, to avoid cross signal by anti-rat Alexa 546, we used a high dilution of anti-CD11b followed by fluorescent signal amplification with TSA kit (Cy5 Tyramide). We have set up the optimal working dilution for anti-CD11b by performing the described protocol except for step 1.17 and using at least 7 different dilutions of anti-CD11b as reported in table 1. As a result, 1:30,000 has been chosen being the only dilution achieving: 1) visible signal with Cy5 at excitation wavelength 646 nm; 2) no signal with Alexa 546 at excitation wavelength 532 nm. In this way, Alexa 546 fluorescent signal is selectively associated with CD68 expression.
The optimal dilutions for anti-CD11b and anti-CD68 antibodies may vary depending on the type of tissue and must be defined prior to start the co-labeling protocol.
<ol>
	<li>Wash brain cryosections twice with PBS.</li>
	<li>Incubate cryosections for 5 min in PBS containing 1% H2O2 (step required since the fluorescent amplification needs incubation with horseradish peroxidase, streptavidin-HRP, see step 1.12).</li>
	<li>Wash cryosections 2x with PBS.</li>
	<li>Incubate cryosections for 60 min in PBS containing 10% NGS and 0.3% Triton.</li>
	<li>Incubate cryosections at 4 &#176;C overnight in PBS containing primary Ab Rat anti-CD11b [1:30,000], 10% NGS and 0.3% Triton.</li>
	<li>Wash cryosections 2x (5 min) with PBS.</li>
	<li>Incubate cryosections for 60 min in PBS containing biotinylated secondary anti-Rat Ab [1:200] and 1% NGS.</li>
	<li>Wash cryosections 2x with PBS.</li>
	<li>Wash cryosections with TNT (Tris-HCl, NaCl, Tween: 0.1 M TRIS-HCl, pH 7.4, 0.15 M NaCl, 0.05% Tween 20).</li>
	<li>Incubate cryosections for 1.5 hr in TNB (Tris-HCl-NaCl-Blocking buffer: 0.1 M TRIS-HCl, pH 7.4, 0.15 M NaCl, 0.5% Blocking reagent from appropriate kit (see table of reagents)).</li>
	<li>Wash cryosections 3x times with TNT.</li>
	<li>Incubate cryosections in TNB containing streptavidin-HRP [1:100].</li>
	<li>Wash cryosections 3x with TNT.</li>
	<li>Incubate cryosections for 8 min in Amplification Diluent containing Cyanine 5 Tyramide [1:300].</li>
	<li>Wash cryosections 3x with PBS.</li>
	<li>Incubate cryosections for 60 min in PBS containing 10% NGS and 0.1% Triton.</li>
	<li>Incubate cryosections at 4 &#176;C overnight in PBS containing primary Ab Rat anti-CD68 [1:200], 3% NGS and 0.3% Triton.</li>
	<li>Wash cryosections 3x with PBS.</li>
	<li>Incubate cryosections for 60 min in PBS containing fluorconjugated secondary Ab Alexa 546 anti-Rat [1:500] and 1% NGS.</li>
	<li>Wash cryosections 3x with PBS.</li>
	<li>Incubate cryosections for 10 min in PBS containing Hoechst 1 &#956;g/ml.</li>
	<li>Wash cryosections 3x with PBS.</li>
	<li>Mount cryosections in Prolong Gold.</li>
</ol>
2. Acquisition of Three-dimensional Images by Confocal Microscopy
The microscope used here was a IX81 microscope equipped with a confocal scan unit FV500 with 3 laser lines: Ar-Kr (488nm), He-Ne red (646nm), and He-Ne green (532nm) and a UV diode.
<ol>
	<li>Select the excitation lasers depending on the wavelengths of the fluorescent dyes to be excited (He-Ne red for Cy5, CD11b; He-Ne green for Alexa546, CD68 and the UV diode for Hoechst, nuclei).</li>
	<li>Select the best dichroic mirror combination for light signal collection.</li>
	<li>Set up image resolution at a minimum of 800 x 600 pixels.</li>
	<li>Identify an area of interest by using epi-fluorescence and progressively increase the magnification to the 40X objective.</li>
	<li>Switch to Laser Scanning Microscopy (LSM) modality.</li>
	<li>Run repetitive scans to adjust the photomultiplier (PMT) and the gain for each channel. Lasers may be turned on individually to facilitate the set up. Keep gain as low as possible to avoid unwanted non-specific signals.</li>
	<li>With repetitive scan running, move the focus control to define lower and upper extremes of the z-axis (total z-axis length = 10 &#956;m).</li>
	<li>Stop repetitive scan.</li>
	<li>Define step size. It should be as close as possible to pixel size (0.225 &#956;m) to obtain a standard 1:1 size ratio over the z-axis.</li>
	<li>Activate Kalman filter at least 2 times.</li>
	<li>Activate sequential scanning mode to avoid bleed-through effects.</li>
	<li>Go half-way along the z-axis and run a xy sequential scan. Check the set-up of PMT and gain (good signal/noise ratio). If not satisfactory, repeat step 2.6.</li>
	<li>Run xyz acquisition.</li>
	<li>Export data as multitiff file. Each multitiff file typically contains 3 color channels (blue, green and red) and 44 focal planes.</li>
</ol>
3. Three-dimensional View of Confocal Acquisitions and Three-dimensional Rendering
Upload multitiff files to Imaris software and process them as follows:
<ol>
	<li>Open software.</li>
	<li>Select the surpass view.</li>
	<li>Upload the multitiff file.</li>
	<li>Select the desired color for each channel.</li>
	<li>Remove noise from background by increasing the minimum value on the display adjustment panel. Adjust each channel individually.</li>
	<li>Go to the section view. Move along the z-axis looking for co-localization (yellow pixels).</li>
	<li>Click on a yellow area to see whether the colocalization is present along the z-axis (i.e. belongs to a solid object). Z-axis projections are visible in the right and bottom part of the figure.</li>
	<li>Take a snapshot.</li>
	<li>Go back to surpass view.</li>
	<li>Crop 3D to isolate a cell or a cluster of cells.</li>
	<li>Select one channel on the display adjustment panel.</li>
	<li>Select the surpass/surfaces algorithm builder. Algorithm steps:
	<ol>
		<li>Select channel.</li>
		<li>Define threshold (use the same minimum value in the display adjustment panel).</li>
		<li>Define resizing.</li>
		<li>Define smoothing (best = 0.200).</li>
		<li>Define color appearance.</li>
		<li>End algorithm.</li>
	</ol>
	</li>
	<li>Repeat step 3.12 for each channel.</li>
	<li>Deselect fluorescence channels on the display adjustment panel and select all the three surfaces.</li>
	<li>Move the volume to find the best view.</li>
	<li>Take a snapshot.</li>
</ol>

<ol>
	<li>Davalos, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ATP+mediates+rapid+microglial+response+to+local+brain+injury+in+vivo.">ATP mediates rapid microglial response to local brain injury in vivo.</a> Nat. Neurosci. 8, 752-758 (2005).</li><li>Yenari, M. A., Kauppinen, T. M., Swanson, R. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microglial+activation+in+stroke:+therapeutic+targets.">Microglial activation in stroke: therapeutic targets.</a> Neurotherapeutics. 7, 378-391 (2010).</li><li>Iadecola, C., Anrather, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+immunology+of+stroke:+from+mechanisms+to+translation.">The immunology of stroke: from mechanisms to translation.</a> Nat. Med. 17, 796-808 (2011).</li><li>Jin, R., Yang, G., Li, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Inflammatory+mechanisms+in+ischemic+stroke:+role+of+inflammatory+cells.">Inflammatory mechanisms in ischemic stroke: role of inflammatory cells.</a> J. Leukoc. Biol. 87, 779-789 (2010).</li><li>Schilling, M., Besselmann, M., Muller, M., Strecker, J. K., Ringelstein, E. B., Kiefer, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Predominant+phagocytic+activity+of+resident+microglia+over+hematogenous+macrophages+following+transient+focal+cerebral+ischemia:+an+investigation+using+green+fluorescent+protein+transgenic+bone+marrow+chimeric+mice.">Predominant phagocytic activity of resident microglia over hematogenous macrophages following transient focal cerebral ischemia: an investigation using green fluorescent protein transgenic bone marrow chimeric mice.</a> Exp. Neurol. 196, 290-297 (2005).</li><li>Perego, C., Fumagalli, S., De Simoni, M. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Temporal+pattern+of+expression+and+colocalization+of+microglia/macrophage+phenotype+markers+following+brain+ischemic+injury+in+mice.">Temporal pattern of expression and colocalization of microglia/macrophage phenotype markers following brain ischemic injury in mice.</a> Journal of Neuroinflammation. 8, 174-193 (2011).</li><li>Zanier, E. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+umbilical+cord+blood+mesenchymal+stem+cells+protect+mice+brain+after+trauma.">Human umbilical cord blood mesenchymal stem cells protect mice brain after trauma.</a> Crit. CareMed. 39 (11), 2501-2510 (2011).</li><li>Capone, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neurosphere+derived+cells+exert+a+neuroprotective+action+by+changing+the+ischemic+microenvironment.">Neurosphere derived cells exert a neuroprotective action by changing the ischemic microenvironment.</a> PLoS ONE. 2, e373 (2007).</li><li>Bhatia, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+host+defense+against+Aspergillus+fumigatus+involves+alveolar+macrophages+with+a+predominance+ofalternatively+activated+phenotype.">Rapid host defense against Aspergillus fumigatus involves alveolar macrophages with a predominance ofalternatively activated phenotype.</a> PLoS One. 6, e15943 (2011).</li><li>Raes, G., Noel, W., Beschin, A., Brys, L., de Baetselier, P., Hassanzadeh, G. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FIZZ1+and+Ym+as+tools+to+discriminate+between+differentially+activated+macrophages.">FIZZ1 and Ym as tools to discriminate between differentially activated macrophages.</a> Dev. Immunol. 9, 151-159 (2002).</li><li>Gesuete, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recombinant+C1+inhibitor+in+brain+ischemic+injury.">Recombinant C1 inhibitor in brain ischemic injury.</a> Ann. Neurol. 66, 332-342 (2009).</li><li>Sica, A., Mantovani, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Macrophages+plasticity+and+polarization:+in+vivo+veritas.">Macrophages plasticity and polarization: in vivo veritas.</a> J. Clin. Invest. 122 (3), 787-795 (2012).</li></ol>

Authors have nothing to disclose.

We present here immunofluorescence-based protocols followed by three-dimensional confocal analysis as a powerful approach to investigate localization and co-expression of M/M phenotype markers into the ischemic area (for a more detailed analysis see ref 6). This method combines specific staining of relevant marker of M/M activation with three-dimensional confocal imaging. The fine tuning of antibodies, serum and fluorconjugated working dilutions allows optimal signal to noise ratio of the investigated m...

After acute brain injury, microglia are rapidly activated and undergo dramatic morphological and phenotypic changes1-3. This intrinsic response is associated to recruitment of blood-born macrophages which migrate into the injured brain parenchyma4,5. The role of microglia and macrophages which are antigenically not distinguishable (henceforth referred to as M/M) in brain injury is still debated. An increasing number of studies indicate that, similarly to what described for peripheral macrophages, microglia and brain recruited macrophages can assume different phenotypes whose extremes correspond to classic pro-inflammatory toxic (M1) or anti-inflammatory protective (M2) phenotype. The different activation states, including secretion of pro- or anti-inflammatory factors, release of neurotrophic molecules and lysosomal activity are characterized by a specific pattern of phenotypic markers, whose expression depends on the temporal evolution of the surrounding environment. The characterization of these M/M phenotypes in the injured brain is still scanty. We used a well-established murine model of pMCAo to analyze M/M expression and evolution after stroke. Immunofluorescence based protocols presented here aim at getting insight into the appearance of specific M/M phenotype markers, their localization and cellular co-expression in the ischemic area. We investigated a few molecules associated to different activation state or phenotype, namely CD11b, a surface marker expressed by leukocytes and a widely used marker of M/M activation/recruitment6-8, CD68 a marker of lysosomes6,7 and Ym1 a secretory protein expressed by alternatively activated (M2) macrophages and associated to recovery and function restoration9-10.	
	When two markers are expressed by the same cell, but in different subcellular compartments, colocalization alone may not be much informative. In this case, analysis of coexpression can be performed by using single plane view and by three-dimensional renderings. We here describe a protocol to obtain a thorough three-dimensional analysis of marker coexpression.

<table><tbody><tr><td colspan="4">&lt;strong&gt;Materials&lt;/strong&gt;</td></tr><tr><td>Rat Anti-mouse CD11b</td><td>Kindly provided by Dr. A. Doni, Istituto Clinico Humanitas, Milan, Italy</td><td></td><td></td></tr><tr><td>Rat Anti-mouse CD68 </td><td>AbD Serotec</td><td>MCA 1957</td><td></td></tr><tr><td>Rabbit Anti-mouse Ym1 </td><td>Stem Cell Technologies</td><td>1404</td><td></td></tr><tr><td>H&amp;#8211;chst 33342</td><td>Life technologies</td><td>H21492</td><td></td></tr><tr><td>Mouse Anti-Neural Nuclei (NeuN)</td><td>CHEMICON</td><td>MAB377</td><td></td></tr><tr><td>Biotinilated Goat Anti-Rat antibody</td><td>Jackson Immuno Research</td><td>112-065-143</td><td></td></tr><tr><td>TSA Cyanine 5 System </td><td>Perkin Elmer</td><td>NEL705A001KT</td><td></td></tr><tr><td>Prolong Gold </td><td>Invitrogen</td><td>P36930</td><td></td></tr><tr><td>Anti-rat alexa 546</td><td>Invitrogen</td><td>A-11081</td><td></td></tr><tr><td>Anti mouse Alexa 488</td><td>Invitrogen</td><td>A-21121</td><td></td></tr><tr><td>Anti-rabbit Alexa 594</td><td>Invitrogen</td><td>A-11037</td><td></td></tr><tr><td>Normal Goat Serum</td><td>Vectors Laboratories</td><td>S-1000</td><td></td></tr><tr><td>Tritin X-100</td><td>Sigma</td><td>T8787</td><td></td></tr><tr><td>Phosphate Buffered Saline</td><td>Sigma</td><td>P4417-100</td><td></td></tr><tr><td colspan="4">&lt;strong&gt;Equipment&lt;/strong&gt;</td></tr><tr><td>Cryostat CM1850</td><td>Leica</td><td></td><td></td></tr><tr><td>Olympus IX81 confocal microscope </td><td>Olympus</td><td></td><td></td></tr><tr><td>AnalySIS software</td><td>Olympus</td><td></td><td></td></tr><tr><td>Imaris software 5.0</td><td>Bitplane</td><td></td><td></td></tr><tr><td>Photoshop cs2</td><td>Adobe Systems</td><td></td><td></td></tr><tr><td>Software packages GraphPad Prism version 4.0</td><td>GraphPad Software Inc.</td><td></td><td></td></tr></tbody></table>

three-dimensional confocal analysis of microglia/macrophage markers of polarization in experimental brain injury

After brain stroke microglia/macrophages (M/M) undergo rapid activation with dramatic morphological and phenotypic changes that include expression of novel surface antigens and production of mediators that build up and maintain the inflammatory response. Emerging evidence indicates that M/M are highly plastic cells that can assume classic pro-inflammatory (M1) or alternative anti-inflammatory (M2) activation after acute brain injury. However a complete characterization of M/M phenotype marker expression, their colocalization and temporal evolution in the injured brain is still missing.	
	Immunofluorescence protocols specifically staining relevant markers of M/M activation can be performed in the ischemic brain. Here we present immunofluorescence-based protocols followed by three-dimensional confocal analysis as a powerful approach to investigate the pattern of localization and co-expression of M/M phenotype markers such as CD11b, CD68, Ym1, in mouse model of focal ischemia induced by permanent occlusion of the middle cerebral artery (pMCAO). Two-dimensional analysis of the stained area reveals that each marker is associated to a defined M/M morphology and has a given localization in the ischemic lesion. Patterns of M/M phenotype marker co-expression can be assessed by three-dimensional confocal imaging in the ischemic area. Images can be acquired over a defined volume (10 &mu;m z-axis and a 0.23 &mu;m step size, corresponding to a 180 x 135 x 10 &mu;m volume) with a sequential scanning mode to minimize bleed-through effects and avoid wavelength overlapping. Images are then processed to obtain three-dimensional renderings by means of Imaris software. Solid view of three dimensional renderings allows the definition of marker expression in clusters of cells. We show that M/M have the ability to differentiate towards a multitude of phenotypes, depending on the location in the lesion site and time after injury.

An example of the results obtained when labeling protocols and confocal acquisitions are carried out into the ischemic region is illustrated in Figures 1A and 1B. A two dimensional view of acquired images shows that at twenty-four hours after ischemia (A), the lysosomal marker CD68 (green) is expressed in hypertrophic ameboid CD11b cells (red) present in the ischemic core. In the border zone (B) CD11b positive cells display round cell bodies and ramified...

Watch this Scientific Journal Video about Three-dimensional Confocal Analysis of Microglia/macrophage Markers of Polarization in Experimental Brain Injury at JoVE.com

Three-dimensional Confocal Analysis of Microglia/macrophage Markers of Polarization in Experimental Brain Injury

A way to gain new insights into the complexity of the brain inflammatory response is presented. We describe immunofluorescence-based protocols followed by three-dimensional confocal analysis to investigate the pattern of co-expression of microglia/macrophage phenotype markers in a mouse model of focal ischemia.

After brain stroke microglia/macrophages (M/M) undergo  rapid activation with dramatic morphological and phenotypic changes that  include expression of ...

three-dimensional-confocal-analysis-microgliamacrophage-markers

Research

JoVE Journal

Neuroscience

11.5K Views.  IRCCS - Istituto di Ricerche Farmacologiche Mario Negri. A way to gain new insights into the complexity of the brain inflammatory response is presented. We describe immunofluorescence-based protocols followed by three-dimensional confocal analysis to investigate the pattern of co-expression of microglia/macrophage phenotype markers in a mouse model of focal ischemia.

Video: Three-dimensional Confocal Analysis of Microglia/macrophage Markers of Polarization in Experimental Brain Injury

Acute Brain Trauma in Mice Followed By Longitudinal Two-photon Imaging

Although acute brain trauma often results from head damage in different accidents and affects a substantial fraction of the population, there is no effective treatment for it yet. Limitations of currently used animal models impede understanding of the pathology mechanism. Multiphoton microscopy allows studying cells and tissues within intact animal brains longitudinally under physiological and pathological conditions. Here, we describe two models of acute brain injury studied by means of two-photon imaging of brain cell behavior under posttraumatic conditions. A selected brain region is injured with a sharp needle to produce a trauma of a controlled width and depth in the brain parenchyma. Our method uses stereotaxic prick with a syringe needle, which can be combined with simultaneous drug application. We propose that this method can be used as an advanced tool to study cellular mechanisms of pathophysiological consequences of acute trauma in mammalian brain in vivo. In this video, we combine acute brain injury with two preparations: cranial window and skull thinning. We also discuss advantages and limitations of both preparations for multisession imaging of brain regeneration after trauma.

Acute brain trauma is a severe injury that has no adequate treatment to date. Multiphoton microscopy allows studying longitudinally the process of acute brain trauma development and probing therapeutical strategies in rodents. Two models of acute brain trauma studied with in vivo two-photon imaging of brain are demonstrated in this protocol.

Although acute brain trauma often results from head damage in different accidents and affects a substantial fraction of the population, there is no ...

Medicine

Intravital Imaging of Axonal Interactions with Microglia and Macrophages in a Mouse Dorsal Column Crush Injury

Traumatic spinal cord injury causes an inflammatory reaction involving blood-derived macrophages and central nervous system (CNS)-resident microglia. Intra-vital two-photon microscopy enables the study of macrophages and microglia in the spinal cord lesion in the living animal. This can be performed in adult animals with a traumatic injury to the dorsal column. Here, we describe methods for distinguishing macrophages from microglia in the CNS using an irradiation bone marrow chimera to obtain animals in which only macrophages or microglia are labeled with a genetically encoded green fluorescent protein. We also describe a injury model that crushes the dorsal column of the spinal cord, thereby producing a simple, easily accessible, rectangular lesion that is easily visualized in an animal through a laminectomy. Furthermore, we will outline procedures to sequentially image the animals at the anatomical site of injury for the study of cellular interactions during the first few days to weeks after injury.

Two-photon intravital imaging can be used to investigate interactions among different cell types in the spinal cord in their native tissue environment in a bone marrow chimeric animal with a dorsal column traumatic spinal cord crush injury.

Traumatic spinal cord injury causes an inflammatory reaction involving blood-derived macrophages and central nervous system (CNS)-resident microglia. ...

Protocol for Three-dimensional Confocal Morphometric Analysis of Astrocytes

As glial cells in the brain, astrocytes have diverse functional roles in the central nervous system. In the presence of harmful stimuli, astrocytes modify their functional and structural properties, a condition called reactive astrogliosis. Here, a protocol for assessment of the morphological properties of astrocytes is presented. This protocol includes quantification of 12 different parameters i.e. the surface area and volume of the tissue covered by an astrocyte (astrocyte territory), the entire astrocyte including branches, cell body, and nucleus, as well as total length and number of branches, the intensity of fluorescence immunoreactivity of antibodies used for astrocyte detection, and astrocyte density (number/1,000 &#181;m2). For this purpose three-dimensional (3D) confocal microscopic images were created, and 3D image analysis software such as Volocity 6.3 was used for measurements. Rat brain tissue exposed to amyloid beta1-40 (A&#946;1-40) with or without a therapeutic&#160;intervention was used to present the method. This protocol can also be used for 3D morphometric analysis of other cells from either in vivo or in vitro conditions.

Astrocytes in the CNS change their functional and structural properties in response to harmful stimuli. This report presents a protocol for assessment of three-dimensional astrocyte morphology in diseased conditions or after therapeutic interventions.

As glial cells in the brain, astrocytes have diverse functional roles in the central nervous system. In the presence of harmful stimuli, astrocytes modify ...

Analysis of Microglia and Monocyte-derived Macrophages from the Central Nervous System by Flow Cytometry

Numerous studies have demonstrated the role of immune cells, in particular macrophages, in central nervous system (CNS) pathologies. There are two main macrophage populations in the CNS: (i) the microglia, which are the resident macrophages of the CNS and are derived from yolk sac progenitors during embryogenesis, and (ii) the monocyte-derived macrophages (MDM), which can infiltrate the CNS during disease and are derived from bone marrow progenitors. The roles of each macrophage subpopulation differ depending on the pathology being studied. Furthermore, there is no consensus on the histological markers or the distinguishing criteria used for these macrophage subpopulations. However, the analysis of the expression profiles of the CD11b and CD45 markers by flow cytometry allows us to distinguish the microglia (CD11b+CD45med) from the MDM (CD11b+CD45high). In this protocol, we show that the density gradient centrifugation and the flow cytometry analysis can be used to characterize these CNS macrophage subpopulations, and to study several markers of interest expressed by these cells as we recently published. Thus, this technique can further our understanding of the role of macrophages in mouse models of neurological diseases and can also be used to evaluate drug effects on these cells.

This protocol provides an analysis of the macrophage subpopulations in the adult mouse central nervous system by flow cytometry and is helpful for the study of multiple markers expressed by these cells.

Numerous studies have demonstrated the role of immune cells, in particular macrophages, in central nervous system (CNS) pathologies. There are two main ...

Immunology and Infection

Stereotactic Atlas-Guided Laser Capture Microdissection of Brain Regions Affected by Traumatic Injury

The ability to isolate specific brain regions of interest can be impeded in tissue disassociation techniques that do not preserve their spatial distribution. Such techniques also potentially skew gene expression analysis because the process itself can alter expression patterns in individual cells. Here we describe a laser capture microdissection (LCM) method to selectively collect specific brain regions affected by traumatic brain injury (TBI) by using a modified Nissl (cresyl violet) staining protocol and the guidance of a rat brain atlas. LCM provides access to brain regions in their native positions and the ability to use anatomical landmarks for identification of each specific region. To this end, LCM has been used previously to examine brain region specific gene expression in TBI. This protocol allows examination of TBI-induced alterations in gene and microRNA expression in distinct brain areas within the same animal. The principles of this protocol can be amended and applied to a wide range of studies examining genomic expression in other disease and/or animal models.

We describe the use of laser capture microdissection to obtain samples of distinct cell populations from different brain regions for gene and microRNA analysis. This technique allows the study of differential effects of traumatic brain injury in specific regions of the rat brain.

The ability to isolate specific brain regions of interest can be impeded in tissue disassociation techniques that do not preserve their spatial ...

Immunofluorescence Staining Using IBA1 and TMEM119 for Microglial Density, Morphology and Peripheral Myeloid Cell Infiltration Analysis in Mouse Brain

This is a protocol for the dual visualization of microglia and infiltrating macrophages in mouse brain tissue. TMEM119 (which labels microglia selectively), when combined with IBA1 (which provides an exceptional visualization of their morphology), allows investigation of changes in density, distribution, and morphology. Quantifying these parameters is important in providing insights into the roles exerted by microglia, the resident macrophages of the brain. Under normal physiological conditions, microglia are regularly distributed in a mosaic-like pattern and present a small soma with ramified processes. Nevertheless, as a response to environmental factors (i.e., trauma, infection, disease, or injury), microglial density, distribution, and morphology are altered in various manners, depending on the insult. Additionally, the described double-staining method allows visualization of infiltrating macrophages in the brain based on their expression of IBA1 and without colocalization with TMEM119. This approach thus allows discrimination between microglia and infiltrating macrophages, which is required to provide functional insights into their distinct involvement in brain homeostasis across various contexts of health and disease. This protocol integrates the latest findings in neuroimmunology that pertain to the identification of selective markers. It also serves as a useful tool for both experienced neuroimmunologists and researchers seeking to integrate neuroimmunology into projects.

This protocol describes a step-by-step workflow for immunofluorescent costaining of IBA1 and TMEM119, in addition to analysis of microglial density, distribution, and morphology, as well as peripheral myeloid cell infiltration in mouse brain tissue.

This is a protocol for the dual visualization of microglia and infiltrating macrophages in mouse brain tissue. TMEM119 (which labels microglia ...

Systems Analysis of the Neuroinflammatory and Hemodynamic Response to Traumatic Brain Injury

Mild traumatic brain injuries (mTBIs) are a significant public health problem. Repeated exposure to mTBI can lead to cumulative, long-lasting functional deficits. Numerous studies by our group and others have shown that mTBI stimulates cytokine expression and activates microglia, decreases cerebral blood flow and metabolism, and impairs cerebrovascular reactivity. Moreover, several works have reported an association between derangements in these neuroinflammatory and hemodynamic markers and cognitive impairments. Herein we detail methods to characterize the neuroinflammatory and hemodynamic tissue response to mTBI in mice. Specifically, we describe how to perform a weight-drop model of mTBI, how to longitudinally measure cerebral blood flow using a non-invasive optical technique called diffuse correlation spectroscopy, and how to perform a Luminex multiplexed immunoassay on brain tissue samples to quantify cytokines and immunomodulatory phospho-proteins (e.g., within the MAPK and NF&#954;B pathways) that respond to and regulate activity of microglia and other neural immune cells. Finally, we detail how to integrate these data using a multivariate systems analysis approach to understand the relationships between all of these variables. Understanding the relationships between these physiologic and molecular variables will ultimately enable us to identify mechanisms responsible for mTBI.

This protocol presents methods to characterize the neuroinflammatory and hemodynamic response to mild traumatic brain injury and to integrate these data as part of a multivariate systems analysis using partial least squares regression.

Mild traumatic brain injuries (mTBIs) are a significant public health problem. Repeated exposure to mTBI can lead to cumulative, long-lasting functional ...

A Preclinical Controlled Cortical Impact Model for Traumatic Hemorrhage Contusion and Neuroinflammation

Cerebral contusion is a severe medical problem affecting millions of people worldwide each year. There is an urgent need to understand the pathophysiological mechanism and to develop effective therapeutic strategy for this devastating neurological disorder. Intraparenchymal hemorrhage and post-traumatic inflammatory response induced by initial physical impact can aggravate microglia/macrophage activation and neuroinflammation which subsequently worsen brain pathology. We provide here a controlled cortical impact (CCI) protocol that can reproduce experimental cortical contusion in mice by using a pneumatic impactor system to deliver mechanical force with controllable magnitude and velocity onto the dural surface. This preclinical model allows researchers to induce moderately severe focal cerebral contusion in mice and to investigate a wide range of post-traumatic pathological progressions including hemorrhage contusion, microglia/macrophage activation, iron toxicity, axonal injury, as well as short-term and long-term neurobehavioral deficits. The present protocol can be useful for exploring the long-term effects of and potential interventions for cerebral contusion.

Intraparenchymal hemorrhage and neuroinflammation accompanied by cerebral contusion can trigger severe secondary brain injury. This protocol details a mouse controlled cortical impact (CCI) model allowing researchers to study hemorrhage contusion and post-traumatic immune responses and explore potential therapeutics.

Cerebral contusion is a severe medical problem affecting millions of people worldwide each year. There is an urgent need to understand the ...

Electromagnetic Controlled Closed-Head Model of Mild Traumatic Brain Injury in Mice

Highly reproducible animal models of traumatic brain injury (TBI), with well-defined pathologies, are needed for testing therapeutic interventions and understanding the mechanisms of how a TBI alters brain function. The availability of multiple animal models of TBI is necessary to model the different aspects and severities of TBI seen in people. This manuscript describes the use of a midline closed head injury (CHI) to develop a mouse model of mild TBI. The model is considered mild because it does not produce structural brain lesions based on neuroimaging or gross neuronal loss. However, a single impact creates enough pathology that cognitive impairment is measurable at least 1 month after injury. A step-by-step protocol to induce a CHI in mice using a stereotaxically guided electromagnetic impactor is defined in the paper. The benefits of the mild midline CHI model include the reproducibility of the injury-induced changes with low mortality. The model has been temporally characterized up to 1 year after the injury for neuroimaging, neurochemical, neuropathological, and behavioral changes. The model is complementary to open skull models of controlled cortical impact using the same impactor device. Thus, labs can model both mild diffuse TBI and focal moderate-to-severe TBI with the same impactor.

The protocol describes mild traumatic brain injury in a mouse model. In particular, a step-by-step protocol to induce a mild midline closed head injury and the characterization of the animal model is fully explained.

Highly reproducible animal models of traumatic brain injury (TBI), with well-defined pathologies, are needed for testing therapeutic interventions and ...

Stab-Wound Mouse Model for Studying Hemorrhage and Inflammation in Traumatic Brain Injury

Traumatic brain injury (TBI) results from physical damage, often caused by accidents or sports-related incidents. The causes of TBI are diverse, including concussions, brain contusions, hematomas, and skull fractures. To replicate these different causes, various TBI mouse models have been developed using distinct protocols. Physical brain injury leads to both primary and secondary brain injuries, which exacerbate neuronal loss. Primary injury occurs immediately after the damage, often due to hemorrhage, and subsequently triggers secondary injuries, including inflammation around the lesion. Developing a TBI model suitable for assessing hemorrhage extension and inflammatory severity is therefore crucial. This protocol introduces a method for mimicking penetrating brain injury, referred to as the stab-wound TBI mouse model, to study mechanisms of hemorrhage, inflammation, and neuronal loss associated with TBI pathology. This model is created by puncturing the skull and brain with needles and is simple to execute without the need for specialized experimental equipment. Additionally, the minor injury inflicted on the mouse cerebral cortex using a needle does not affect the animal's behavior post-surgery. This feature allows researchers to study the localized effects of brain injury without concerns about broader behavioral consequences. Sample data from stab-wounded mouse cerebral cortices demonstrate the model's effectiveness in assessing blood leakage into the parenchyma, glial activation, and inflammatory cytokine production. Furthermore, this protocol facilitates the evaluation of blood coagulants and anti-inflammatory compounds, aiding in the development of therapeutic agents for TBI.

Simplified traumatic brain injury (TBI) models have facilitated the development of therapeutic approaches. This protocol outlines the creation of a stab-wound mouse cortex using needles, enabling the analysis of hemorrhage and inflammation. The stab-wound TBI mouse model offers the advantage of being performed without requiring specialized equipment.

Traumatic brain injury (TBI) results from physical damage, often caused by accidents or sports-related incidents. The causes of TBI are diverse, including ...