This study was funded by Boston Children&#8217;s Hospital start-up funds to A.B., ALSA grant nr. 17-IIP-343 to M.P., and the Office of the Assistant Secretary of Defense for Health Affairs through the Amyotrophic Lateral Sclerosis Research Program under Award No. W81XWH-17-1-0036 to M.P. We acknowledge DFCI Flow Cytometry Core for technical support.

All methods described here have been approved by the Institutional Animal Care and Use Committee (IACUC) of Dana Farber Cancer Institute (protocol number 16-024).
1. Preparation of solutions needed for the experiment
<ol>
	<li>Prepare 1x Hank&#8217;s balanced salt solution (HBSS) by diluting 10x HBSS with sterile water. Pre-chill the solution on ice. At least 25 mL of solution are needed for each sample.</li>
	<li>Prepare isotonic Percoll solution (IPS) by mixing 10x sterile HBSS 1:10 with density gradient medium (i.e., Percoll). Pre-chill on ice. 
	NOTE: IPS can be stored for up to 30 days at 4 &#176;C.</li>
	<li>Prepare flow cytometry (FACS) blocking (BL) solution (1% bovine serum albumin [BSA], 5% fetal bovine serum [FBS] in phosphate-buffered saline [PBS]). Pre-chill on ice.</li>
</ol>
2. Animal euthanasia by intracardiac perfusion and tissue dissection
NOTE: Eight-week-old C57BL/6J mice, either sex, were used in the experiments. Perfusion with PBS solution is performed to eliminate blood contamination from organs, before proceeding with tissue digestion.
<ol>
	<li>Anesthetize the mouse by using a mixture of ketamine/xylazine (90&#8722;200 mg/kg ketamine, 10 mg/kg xylazine). Place the mouse on its back and tape each limb down to the support. Verify adequate depth of anesthesia by checking the withdrawal reflex.</li>
	<li>Make a midline skin incision at the level of the thoracic inlet to expose the sternum. Use forceps to grasp the tip of the sternum, then make one 1 cm incision on each side of the rib cage. Finally cut through the diaphragm and open the sternum widely enough to visualize the heart.</li>
	<li>Use forceps to gently grasp the heart by the right ventricle and lift it to the midline and slightly out of the chest.</li>
	<li>Insert a 23 G butterfly needle into the tip of the left ventricle, towards the aorta and hold firmly.</li>
	<li>Start the perfusion with 1x PBS. Pierce through the right auricle using scissors to allow the perfusate to exit the circulation. Set the flow rate of PBS at 3 mL/min. Perfuse with at least 15 mL of 1x PBS to ensure tissues are clear. 
	NOTE: Blanching of the liver and mesenteric blood vessels are signs of good perfusion. If necessary, the volume of prefusion can be increased up until the fluid exiting the heart is clear of blood, at which point the flush line can be stopped.</li>
	<li>After perfusion, sever the brain from the spinal cord and remove the brain from the skull with scissors and forceps. Remove the fur to increase visibility and control during the dissection and to avoid carrying over hair contaminants. Flush the spinal cord out of its column by using a 3 mL syringe filled with PBS.</li>
	<li>Transfer each tissue in a well of a 6-well multi-well plate prefilled with 2 mL of ice-cold 1x HBSS and keep on ice until digestion.</li>
	<li>Divide the brain and the spinal cord into two halves, along the longitudinal line. 
	NOTE: One half of each tissue is homogenized (see sections below) to allow flow cytometric analyses; the other half can be assigned to different processing for alternative analyses (e.g., dipped in paraformaldehyde fixative solution for histology).</li>
</ol>
3. Enzymatic digestion of brain and spinal cord
NOTE: Volumes described in this section are enough for digestion of one-half brain or spinal cord.
<ol>
	<li>Use a pair of scissors to mince the tissues into 1&#8722;2 mm thick pieces.</li>
	<li>Cut the tip of a 1000 &#181;L pipette with a pair of scissors to make it sufficiently large to allow the collection of the tissue pieces. Pre-rinse the pipette tip with 1x HBSS. Then use the pipette to transfer the 2 mL of HBSS solution containing the minced tissue to a 15 mL conical tube. 
	NOTE: Pre-rinsing of the pipette tip is important to prevent stickiness of the tissue pieces inside the tip.</li>
	<li>Wash the well with additional 2 mL of ice-cold 1x HBSS and transfer the solution to the corresponding 15 mL conical tube containing the tissue pieces.</li>
	<li>Centrifuge each sample for 5 min at 250 x g at 4 &#176;C.</li>
	<li>Prepare enzyme mix 1 of the neural tissue dissociation kit (NTDK; Table of Materials) by mixing 50 &#181;L of enzyme P with 1900 &#181;L of buffer X per sample. Warm enzyme mix 1 at 37 &#176;C in a water bath. Incubate enzyme mix 1 at 37 &#176;C for at least 10 min before use in order to allow for the full activation of the enzyme.</li>
	<li>Aspirate the supernatant from the 15 mL conical tube and add 1.95 mL of enzyme mix 1 to each sample. Gently vortex to make sure the pellet is resuspended.</li>
	<li>Incubate the samples on a wheel or shaker for 15 min at 37 &#176;C.</li>
	<li>In the meanwhile, prepare enzyme mix 2 of the NTDK by mixing 10 &#181;L of enzyme A with 20 &#181;L of buffer Y per sample; pre-warm the solution at 37 &#176;C in a water bath.</li>
	<li>At the end of the incubation with enzyme mix 1, add 30 &#181;L of enzyme mix 2 to each sample.</li>
	<li>Gently mix the samples by pipetting up and down with a 1000 &#181;L pipette tip pre-rinsed with 1x HBSS.</li>
	<li>Incubate the sample on a wheel or shaker for 15 min at 37 &#176;C.</li>
	<li>After incubation, add 10 mL of ice-cold 1x HBSS to each tube to inactivate enzyme mix 1 and enzyme mix 2.</li>
	<li>Centrifuge each sample for 10 min at 320 x g at 4 &#176;C.</li>
	<li>Discard the supernatant; add ice-cold 1x HBSS to each tube up to a final volume of 7 mL and gently resuspend the pellet by vortexing.</li>
	<li>Continue to section 5 for debris removal.</li>
</ol>
4. Mechanical homogenization of brain and spinal cord
NOTE: Volumes described in this section are enough for homogenization of one-half brain or spinal cord. The protocol described in this section can be used as a method alternative to the one described in section 3, depending on user need as discussed below.
<ol>
	<li>Pre-chill the glass mortar of the Dounce tissue grinder (Table of Materials) set on ice.</li>
	<li>Add 3 mL of pre-chilled 1x HBSS to the mortar.</li>
	<li>Transfer the tissue (brain or spinal cord) from the well of the 6-well plate into the glass mortar making sure it is dipped in 1x HBSS and sits at the bottom of the mortar.</li>
	<li>Gently smash the tissue with 10 strokes of pestle A followed by 10 strokes of pestle B. Transfer the homogenized mix into a new 15 mL conical tube.</li>
	<li>Fill the tube to a final volume of 10 mL by using pre-chilled 1x HBSS and centrifuge for 10 min at 320 x g at 4 &#176;C.</li>
	<li>Aspirate the supernatant and add ice-cold 1x HBSS to each tube up to a final volume of 7 mL and gently resuspend the pellet by vortexing.</li>
	<li>Continue to section 5 for debris removal.</li>
</ol>
5. Debris removal
NOTE: Removal of debris, composed mainly of undigested tissue and myelin sheaths, is a critical step to allow efficient staining of the tissue homogenate for subsequent flow cytometric analyses.
<ol>
	<li>Filter each sample through a 70 &#181;m cell strainer to remove any undigested tissue chunk. This step is particularly important especially when working with spinal cord tissues since these samples are more likely to contain undigested nerve fragments or meninges that could affect the subsequent steps.</li>
	<li>Make sure that the final volume is 7 mL in each sample tube. If not, fill with ice-cold 1x HBSS up to 7 mL.</li>
	<li>Add 3 mL of pre-chilled IPS to each sample to make a final volume of 10 mL of a solution containing density gradient medium at 30% final concentration. Gently vortex the samples to make sure they are homogenously mixed.</li>
	<li>Centrifuge samples for 15 min at 700 x g at 18 &#176;C making sure to set the acceleration of the centrifuge to 7 and the brake to 0. 
	NOTE: Centrifugation should take approximately 30 min.</li>
	<li>Delicately remove the samples from the centrifuge. 
	NOTE: A whitish disk composed of debris and myelin should be visible floating on the surface of the solution. A pellet (containing the cells of interest) should be visible at the bottom of the tube.</li>
	<li>Carefully aspirate all the whitish disk of debris and then the rest of the supernatant making sure not to dislodge the pellet. Leave about 100 &#181;L of solution on top of the cell pellet to avoid the risk of inadvertently dislodging it.</li>
	<li>Add 1 mL of FACS BL, resuspend the pellet by pipetting up and down with a 1000 &#181;L pipette tip and transfer samples to 1.5 mL tubes.</li>
	<li>Centrifuge for 5 min at 450 x g at room temperature (RT).</li>
	<li>Gently aspirate the supernatant and resuspend the pellet in appropriate buffer compatible with downstream analyses (see section 6 for the protocol used for flow cytometric evaluation of multiple cell types).</li>
</ol>
6. Staining for flow cytometric evaluation of multiple cell types
<ol>
	<li>Resuspend the pellet obtained in step 5.9 with 350 &#181;L of FACS BL. Add Fc-block to each sample at a final concentration of 5 &#181;g/mL. 
	NOTE: At least 100 &#181;L of the sample should be used for one staining, to make sure to process enough cells to allow reliable analyses.</li>
	<li>Incubate the sample for 10 min at 4 &#176;C before proceeding with the staining.</li>
	<li>Prepare an antibody mix according to Table 1.</li>
	<li>Add antibody mix to each tube, vortex for 5 s and incubate the samples for 15 min at 4 &#176;C in the dark.</li>
	<li>Add 1 mL of PBS to each tube, vortex and centrifuge for 5 min at 450 x g at RT.</li>
	<li>Meanwhile prepare streptavidin mix according to Table 1.</li>
	<li>Discard the supernatant and resuspend the pellet in the streptavidin mix prepared in step 6.6. For each sample, use the same volume as the one used for the staining in step 6.4.</li>
	<li>Vortex for 5 s and incubate the samples for 10 min at 4 &#176;C in the dark.</li>
	<li>Add 1 mL of PBS to each tube, vortex and centrifuge for 5 min at 450 x g at RT.</li>
	<li>Discard the supernatant and resuspend the pellet in FACS BL. Use 300 &#181;L of FACS BL for each 100 &#181;L of sample stained.</li>
	<li>Add 7-amino-actinomycin D (7-AAD) solution to each sample. Use 5 &#181;L of 7-AAD for each 300 &#181;L of sample prepared in step 6.10.</li>
	<li>Store samples at 4 &#176;C in the dark until cytofluorimetric analysis. Perform the analysis within 16 h from sample preparation, to guarantee &#62;60% cell viability.</li>
</ol>

<ol>
	<li>Deverman, B. E., Ravina, B. M., Bankiewicz, K. S., Paul, S. M., Sah, D. W. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gene+therapy+for+neurological+disorders:+progress+and+prospects.">Gene therapy for neurological disorders: progress and prospects.</a> Nature Reviews Drug Discovery. 17 (9), 641-659 (2018).</li><li>Teleanu, D., Negut, I., Grumezescu, V., Grumezescu, A., Teleanu, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanomaterials+for+Drug+Delivery+to+the+Central+Nervous+System.">Nanomaterials for Drug Delivery to the Central Nervous System.</a> Nanomaterials. 9 (3), 371 (2019).</li><li>Chen, 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=Recombinant+Viral+Vectors+as+Neuroscience+Tools.">Recombinant Viral Vectors as Neuroscience Tools.</a> Current Protocols in Neuroscience. 87 (1), 67 (2019).</li><li>Alves, 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=Ultramicroscopy+as+a+novel+tool+to+unravel+the+tropism+of+AAV+gene+therapy+vectors+in+the+brain.">Ultramicroscopy as a novel tool to unravel the tropism of AAV gene therapy vectors in the brain.</a> Scientific Reports. 6 (1), 28272 (2016).</li><li>Peviani, M., 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=Lentiviral+vectors+carrying+enhancer+elements+of+Hb9+promoter+drive+selective+transgene+expression+in+mouse+spinal+cord+motor+neurons.">Lentiviral vectors carrying enhancer elements of Hb9 promoter drive selective transgene expression in mouse spinal cord motor neurons.</a> Journal of Neuroscience Methods. 205 (1), 139-147 (2012).</li><li>Baumgarth, N., Roederer, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+practical+approach+to+multicolor+flow+cytometry+for+immunophenotyping.">A practical approach to multicolor flow cytometry for immunophenotyping.</a> Journal of Immunological Methods. 243 (1-2), 77-97 (2000).</li><li>Sykora, M. M., Reschke, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immunophenotyping+of+Tissue+Samples+Using+Multicolor+Flow+Cytometry.">Immunophenotyping of Tissue Samples Using Multicolor Flow Cytometry.</a> Methods in Molecular Biology. 1953, 253-268 (2019).</li><li>Legroux, L., 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=An+optimized+method+to+process+mouse+CNS+to+simultaneously+analyze+neural+cells+and+leukocytes+by+flow+cytometry.">An optimized method to process mouse CNS to simultaneously analyze neural cells and leukocytes by flow cytometry.</a> Journal of Neuroscience Methods. 247, 23-31 (2015).</li><li>Lee, J. K., Tansey, 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=Microglia+Isolation+from+Adult+Mouse+Brain.">Microglia Isolation from Adult Mouse Brain.</a> Methods in Molecular Biology. 1041, 17-23 (2013).</li><li>Grabert, K., McColl, B. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+and+Phenotyping+of+Adult+Mouse+Microglial+Cells.">Isolation and Phenotyping of Adult Mouse Microglial Cells.</a> Methods in Molecular Biology. 1784, 77-86 (2018).</li><li>Nikodemova, M., Watters, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Efficient+isolation+of+live+microglia+with+preserved+phenotypes+from+adult+mouse+brain.">Efficient isolation of live microglia with preserved phenotypes from adult mouse brain.</a> Journal of Neuroinflammation. 9 (1), 635 (2012).</li><li>Garcia, J. A., Cardona, S. M., Cardona, A. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+and+analysis+of+mouse+microglial+cells.">Isolation and analysis of mouse microglial cells.</a> Current Protocols in Immunology. 104 (1), 1-15 (2014).</li><li>Papa, 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=Selective+Nanovector+Mediated+Treatment+of+Activated+Proinflammatory+Microglia/Macrophages+in+Spinal+Cord+Injury.">Selective Nanovector Mediated Treatment of Activated Proinflammatory Microglia/Macrophages in Spinal Cord Injury.</a> ACS Nano. 7 (11), 9881-9895 (2013).</li><li>Peviani, M., 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=Neuroprotective+effects+of+the+Sigma-1+receptor+(S1R)+agonist+PRE-084,+in+a+mouse+model+of+motor+neuron+disease+not+linked+to+SOD1+mutation.">Neuroprotective effects of the Sigma-1 receptor (S1R) agonist PRE-084, in a mouse model of motor neuron disease not linked to SOD1 mutation.</a> Neurobiology of Disease. 62, 218-232 (2014).</li><li>Peviani, M., 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=Biodegradable+polymeric+nanoparticles+administered+in+the+cerebrospinal+fluid:+Brain+biodistribution,+preferential+internalization+in+microglia+and+implications+for+cell-selective+drug+release.">Biodegradable polymeric nanoparticles administered in the cerebrospinal fluid: Brain biodistribution, preferential internalization in microglia and implications for cell-selective drug release.</a> Biomaterials. 209, 25-40 (2019).</li><li>Meng, F., 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=CD73-derived+adenosine+controls+inflammation+and+neurodegeneration+by+modulating+dopamine+signalling.">CD73-derived adenosine controls inflammation and neurodegeneration by modulating dopamine signalling.</a> Brain. 142 (3), 700-718 (2019).</li><li>Nedeljkovic, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Complex+regulation+of+ecto-5'-nucleotidase/CD73+and+A2AR-mediated+adenosine+signaling+at+neurovascular+unit:+A+link+between+acute+and+chronic+neuroinflammation.">Complex regulation of ecto-5'-nucleotidase/CD73 and A2AR-mediated adenosine signaling at neurovascular unit: A link between acute and chronic neuroinflammation.</a> Pharmacological Research. 144, 99-115 (2019).</li></ol>

The authors have nothing to disclose.

Herein we describe a protocol for the co-purification and concurrent flow cytometric analysis of some of the most relevant CNS cells from mouse brain and spinal cord. Traditionally, histological analyses have been applied to describe the distribution of nanoparticles or the transduction efficiency of viral vectors in the CNS5,13, or to provide insights on morphological and molecular changes occurring in specific cell types during a pathology or upon pharmacologic...

Gene and drug delivery technologies (such as viral vectors and nanoparticles) have become a powerful tool that can be applied to gain better insights on specific molecular pathways altered in neurodegenerative diseases and for development of innovative therapeutic approaches1,2,3. Optimization of these tools relies on quantification of: (1) the extent of penetration in the CNS upon different routes of administration and (2) targeting of specific cell populations. Histological analyses are usually applied to visualize fluorescent reporter genes or fluorescently-tagged nanoparticles in different CNS areas and across different cell types, identified by immunostaining for specific cell markers4,5. Even though this approach provides valuable information on the biodistribution of the administered gene or drug-delivery tools, the technique can be time-consuming and labor-intense since it requires: (1) tissue fixation, cryopreservation or paraffin-embedding and slicing; (2) staining for specific cellular markers sometimes requiring antigen retrieval; (3) acquisition by fluorescence microscopy, which usually allows the analysis of a limited number of different markers within the same experiment; (4) image processing to allow proper quantification of the signal of interest.
Flow cytometry has become a widely used technique which takes advantage of very specific fluorescent markers to allow not only a rapid quantitative evaluation of different cell phenotypes in cell suspensions, based on expression of surface or intracellular antigens, but also functional measurements (e.g., rate of apoptosis, proliferation, cell cycle analysis, etc.). Physical isolation of cells through fluorescent activated cell sorting is also possible, allowing further downstream applications (e.g., cell culture, RNAseq, biochemical analyses etc.)6,7,8.
Tissue homogenization is a critical step necessary to obtain a single cell suspension to allow reliable and reproducible downstream flow cytometric evaluations. Different methods have been described for adult brain-tissue homogenization, mainly with the aim to isolate microglia cells9,10,11; they can be overall classified in two main categories: (1) mechanical dissociation, which uses grinding or shearing force through a Dounce homogenizer (DH) to rip apart cells from their niches and form a relatively homogenized single cell suspension, and (2) enzymatic digestion, which relies on incubation of minced tissue chunks at 37 &#176;C in the presence of proteolytic enzymes, such as trypsin or papain, favoring the degradation of the extracellular matrix to create a fairly homogenized cell suspension12.
Regardless of which method is utilized, a purification step is recommended after tissue homogenization to remove myelin through centrifugation on a density gradient or by magnetic selection9,12, before moving to the downstream applications.
Here, we describe a tissue processing method based on papain digestion (PD) followed by purification on a density gradient, optimized to obtain viable heterogeneous cell suspensions from mouse brain or spinal cord in a time-sensitive manner and suitable for flow cytometry. Moreover, we describe a 9-color flow cytometry panel and the gating strategy we adopted in the laboratory to allow the simultaneous discrimination of different CNS populations, live/dead cells or positivity for fluorescent reporters such as green fluorescent protein or rhodamine dye. By applying this flow cytometric analysis, we can compare different methods of tissue processing, i.e., PD versus DH, in terms of preservation of cellular viability and yields of different cell types.
The details we provide herein can instruct decision on the homogenization protocol and the antibody combination to use in the flow cytometry panel, based on the specific cell type(s) of interest and the downstream analyses (e.g., temperature-sensitive applications, tracking of specific fluorescent markers, in vitro culture, functional analyses).

<table>
	<tbody>
		<tr>
			<td>10X HBSS (Calcium, Magnesium chloride, and Magnesium Sulfate-free)</td>
			<td>Gibco</td>
			<td>14185-052</td>
			<td></td>
		</tr>
		<tr>
			<td>70 mm Cell Strainer</td>
			<td>Corning</td>
			<td>431751</td>
			<td></td>
		</tr>
		<tr>
			<td>ACSA/ACSA2 anti-mouse antibody</td>
			<td>Miltenyi Biotec</td>
			<td>130-117-535</td>
			<td>APC conjugated</td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin</td>
			<td>Sigma Aldrich</td>
			<td>A9647-1KG</td>
			<td></td>
		</tr>
		<tr>
			<td>CD11b rat anti-mouse antibody</td>
			<td>Invitrogen</td>
			<td>47-0112-82</td>
			<td>APC-eFluor 780 conjugated</td>
		</tr>
		<tr>
			<td>CD31 rat anti-mouse antibody</td>
			<td>BD Bioscience</td>
			<td>562939</td>
			<td>BV421 conjugated</td>
		</tr>
		<tr>
			<td>CD45 rat anti-mouse antibody</td>
			<td>Biolegend</td>
			<td>103138</td>
			<td>Brilliant Violet 510 conjugated</td>
		</tr>
		<tr>
			<td>CD90.1/Thy1.1 rat anti-mouse antibody</td>
			<td>Biolegend</td>
			<td>202518</td>
			<td>PE/Cy7 conjugated</td>
		</tr>
		<tr>
			<td>CD90.2/Thy1.2 rat anti-mouse antibody</td>
			<td>Biolegend</td>
			<td>1005325</td>
			<td>PE/Cy7 conjugated</td>
		</tr>
		<tr>
			<td>Conical Tubes (15 mL)</td>
			<td>CellTreat</td>
			<td>229411</td>
			<td></td>
		</tr>
		<tr>
			<td>Conical Tubes (50 mL)</td>
			<td>CellTreat</td>
			<td>229422</td>
			<td></td>
		</tr>
		<tr>
			<td>Dounce Tissue Grinder set (Includes Mortar as well as Pestles A and B)</td>
			<td>Sigma-Aldrich</td>
			<td>D9063-1SET</td>
			<td></td>
		</tr>
		<tr>
			<td>Fc (CD16/CD32) Block rat anti-mouse antibody</td>
			<td>BD Pharmingen</td>
			<td>553142</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Benchmark</td>
			<td>100-106</td>
			<td></td>
		</tr>
		<tr>
			<td>Neural Tissue Dissociation Kit (P)</td>
			<td>Miltenyi Biotec</td>
			<td>130-092-628</td>
			<td></td>
		</tr>
		<tr>
			<td>O4 anti mouse/rat/human antibody</td>
			<td>Miltenyi Biotec</td>
			<td>130-095-895</td>
			<td>Biotin conjugated</td>
		</tr>
		<tr>
			<td>Percoll</td>
			<td>GE Healthcare</td>
			<td>10266569</td>
			<td>sold as not sterile reagent</td>
		</tr>
		<tr>
			<td>Percoll</td>
			<td>Sigma</td>
			<td>65455529</td>
			<td>sterile reagent (to be used for applications requiring sterility)</td>
		</tr>
		<tr>
			<td>Percoll PLUS</td>
			<td>Sigma</td>
			<td>GE17-5445-01</td>
			<td>reagent containing very low traces of endotoxin</td>
		</tr>
		<tr>
			<td>Streptavidin</td>
			<td>Invitrogen</td>
			<td>S3258</td>
			<td>Alexa Fluor 680 conjugated</td>
		</tr>
	</tbody>
</table>

simultaneous flow cytometric characterization of multiple cell types retrieved from mouse brain/spinal cord through different homogenization methods

Recent advances in viral vector and nanomaterial sciences have opened the way for new cutting-edge approaches to investigate or manipulate the central nervous system (CNS). However, further optimization of these technologies would benefit from methods allowing rapid and streamline determination of the extent of CNS and cell-specific targeting upon administration of viral vectors or nanoparticles in the body. Here, we present a protocol that takes advantage of the high throughput and multiplexing capabilities of flow cytometry to allow a straightforward quantification of different cell subtypes isolated from mouse brain or spinal cord, namely microglia/macrophages, lymphocytes, astrocytes, oligodendrocytes, neurons and endothelial cells. We apply this approach to highlight critical differences between two tissue homogenization methods in terms of cell yield, viability and composition. This could instruct the user to choose the best method depending on the cell type(s) of interest and the specific application. This method is not suited for analysis of anatomical distribution, since the tissue is homogenized to generate a single-cell suspension. However, it allows to work with viable cells and it can be combined with cell-sorting, opening the way for several applications that could expand the repertoire of tools in the hands of the neuroscientist, ranging from establishment of primary cultures derived from pure cell populations, to gene-expression analyses and biochemical or functional assays on well-defined cell subtypes in the context of neurodegenerative diseases, upon pharmacological treatment or gene therapy.

We compared two different homogenization methods (DH versus PD) applied to mouse brain and spinal cord, to test the efficiency in retrieving different viable cell types suitable for downstream applications. To do so, we exploited a 9-color flow cytometry panel designed to characterize, in the same sample, different CNS cell types including microglia, lymphocytes, neurons, astrocytes, oligodendrocytes and endothelium.
Brain and spinal cord tissues were retrieved from different mice (n &#8805; 6...

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Simultaneous Flow Cytometric Characterization of Multiple Cell Types Retrieved from Mouse Brain/Spinal Cord Through Different Homogenization Methods

We present a flow cytometry method to identify simultaneously different cell types retrieved from mouse brain or spinal cord. This method could be exploited to isolate or characterize pure cell populations in neurodegenerative diseases or to quantify the extent of cell targeting upon in vivo administration of viral vectors or nanoparticles.

Recent advances in viral vector and nanomaterial sciences have opened the way for new cutting-edge approaches to investigate or manipulate the central ...

simultaneous-flow-cytometric-characterization-multiple-cell-types

Universidad de Cartagena UDEC

Research

JoVE Journal

Medicine

13.4K Views.  Dana-Farber/Boston Children's Cancer and Blood Disorders Center. We present a flow cytometry method to identify simultaneously different cell types retrieved from mouse brain or spinal cord. This method could be exploited to isolate or characterize pure cell populations in neurodegenerative diseases or to quantify the extent of cell targeting upon in vivo administration of viral vectors or nanoparticles.

Video: Simultaneous Flow Cytometric Characterization of Multiple Cell Types Retrieved from Mouse Brain/Spinal Cord Through Different Homogenization Methods

Acute and Chronic Tactile Sensory Testing after Spinal Cord Injury in Rats

Spinal cord injury (SCI) impairs sensory systems causing allodynia1-8. To identify cellular and molecular causes of allodynia, sensitive and valid sensory testing in rat SCI models is needed. However, until recently, no single testing approach had been validated for SCI so that standardized methods have not been implemented across labs. Additionally, available testing methods could not be implemented acutely or when severe motor impairments existed, preventing studies of the development of SCI-induced allodynia3. Here we present two validated sensory testing methods using von Frey Hair (VFH) monofilaments which quantify changes in tactile sensory thresholds after SCI4-5. One test is the well-established Up-Down test which demonstrates high sensitivity and specificity across different SCI severities when tested chronically5. The other test is a newly-developed dorsal VFH test that can be applied acutely after SCI when allodynia develops, prior to motor recovery4-5. Each VFH monofilament applies a calibrated force when touched to the skin of the hind paw until it bends. In the up-down method, alternating VFHs of higher or lower forces are used on the plantar L5 dermatome to delineate flexor withdrawal thresholds. Successively higher forces are applied until withdrawal occurs then lower force VFHs are used until withdrawal ceases. The tactile threshold reflects the force required to elicit withdrawal in 50% of the stimuli. For the new test, each VFH is applied to the dorsal L5 dermatome of the paw while the rat is supported by the examiner. The VFH stimulation occurs in ascending order of force until at least 2 of 3 applications at a given force produces paw withdrawal. Tactile sensory threshold is the lowest force to elicit withdrawal 66% of the time. Acclimation, testing and scoring procedures are described. Aberrant trials that require a retest and typical trials are defined. Animal use was approved by Ohio State University Animal Care and Use Committee.

We describe two tactile sensory testing methods for acute or chronic periods of spinal cord injury in rats. These validated procedures can detect the development and maintenance of allodynia-like sensations.

Spinal cord injury (SCI) impairs sensory systems causing allodynia1-8. To identify cellular and molecular causes of allodynia, sensitive and valid sensory ...

Isolation, Characterization and Comparative Differentiation of Human Dental Pulp Stem Cells Derived from Permanent Teeth by Using Two Different Methods

Developing wisdom teeth are easy-accessible source of stem cells during the adulthood which could be obtained by routine orthodontic treatments. Human pulp-derived stem cells (hDPSCs) possess high proliferation potential with multi-lineage differentiation capacity compare to the ordinary source of adult stem cells1-8; therefore, hDPSCs could be the good candidates for autologous transplantation in tissue engineering and regenerative medicine. Along with these benefits, possessing the mesenchymal stem cells (MSC) features, such as immunolodulatory effect, make hDPSCs more valuable, even in the case of allograft transplantation6,9,10. Therefore, the primary step for using this source of stem cells is to select the best protocol for isolating hDPSCs from pulp tissue. In order to achieve this goal, it is crucial to investigate the effect of various isolation conditions on different cellular behaviors, such as their common surface markers &amp; also their differentiation capacity.
Thus, here we separate human pulp tissue from impacted third molar teeth, and then used both existing protocols based on literature, for isolating hDPSCs,11-13 i.e. enzymatic dissociation of pulp tissue (DPSC-ED) or outgrowth from tissue explants (DPSC-OG). In this regards, we tried to facilitate the isolation methods by using dental diamond disk. Then, these cells characterized in terms of stromal-associated Markers (CD73, CD90, CD105 &amp; CD44), hematopoietic/endothelial Markers (CD34, CD45 &amp; CD11b), perivascular marker, like CD146 and also STRO-1. Afterwards, these two protocols were compared based on the differentiation potency into odontoblasts by both quantitative polymerase chain reaction (QPCR) &amp; Alizarin Red Staining. QPCR were used for the assessment of the expression of the mineralization-related genes (alkaline phosphatase; ALP, matrix extracellular phosphoglycoprotein; MEPE &amp; dentin sialophosphoprotein; DSPP).14

The method described isolation and characterization of human Dental Pulp Stem Cells (hDPSCs) by using either enzymatic dissociation of pulp (DPSC-ED) or direct outgrowth of stem cells from pulp tissue explants (DPSC-OG). Then followed by in vitro comparative differentiation of both types of hDPSCs into odontoblasts.

Developing wisdom teeth are easy-accessible source of stem cells during the adulthood which could be obtained by routine orthodontic treatments. Human ...

Collection, Isolation, and Flow Cytometric Analysis of Human Endocervical Samples

Despite the public health importance of mucosal pathogens (including HIV), relatively little is known about mucosal immunity, particularly at the female genital tract (FGT). Because heterosexual transmission now represents the dominant mechanism of HIV transmission, and given the continual spread of sexually transmitted infections (STIs), it is critical to understand the interplay between host and pathogen at the genital mucosa. The substantial gaps in knowledge around FGT immunity are partially due to the difficulty in successfully collecting and processing mucosal samples. In order to facilitate studies with sufficient sample size, collection techniques must be minimally invasive and efficient. To this end, a protocol for the collection of cervical cytobrush samples and subsequent isolation of cervical mononuclear cells (CMC) has been optimized. Using ex vivo flow cytometry-based immunophenotyping, it is possible to accurately and reliably quantify CMC lymphocyte/monocyte population frequencies and phenotypes. This technique can be coupled with the collection of cervical-vaginal lavage (CVL), which contains soluble immune mediators including cytokines, chemokines and anti-proteases, all of which can be used to determine the anti- or pro-inflammatory environment in the vagina.

The use of cytobrush sampling to collect lymphocytes and monocytes from the endocervix is a minimally invasive technique that provides samples for analysis of female genital tract immunity. In this protocol, we describe the collection of cytobrush samples and immune cell isolation for flow cytometry assays.

Despite the public health importance of mucosal pathogens (including HIV), relatively little is known about mucosal immunity, particularly at the female ...

A Radio-telemetric System to Monitor Cardiovascular Function in Rats with Spinal Cord Transection and Embryonic Neural Stem Cell Grafts

High thoracic or cervical spinal cord injury (SCI) can lead to cardiovascular dysfunction. To monitor cardiovascular parameters, we implanted a catheter connected to a radio transmitter into the femoral artery of rats that underwent a T4 spinal cord transection with or without grafting of embryonic brainstem-derived neural stem cells expressing green fluorescent protein. Compared to other methods such as cannula insertion or tail-cuff, telemetry is advantageous to continuously monitor blood pressure and heart rate in freely moving animals. It is also capable of long term multiple data acquisitions. In spinal cord injured rats, basal cardiovascular data under unrestrained condition and autonomic dysreflexia in response to colorectal distension were successfully recorded. In addition, cardiovascular parameters before and after SCI can be compared in the same rat if a transmitter is implanted before a spinal cord transection. One limitation of the described telemetry procedure is that implantation in the femoral artery may influence the blood supply to the ipsilateral hindlimb.

We present a protocol for using a radio-telemetric system to record cardiovascular parameters in T4 spinal cord transected rats eight weeks after embryonic brainstem neural stem cell grafting into the lesion site. Telemetry is an advanced technique to accurately evaluate cardiovascular function in conscious freely moving spinal cord injured rats.

High thoracic or cervical spinal cord injury (SCI) can lead to cardiovascular dysfunction. To monitor cardiovascular parameters, we implanted a catheter ...

Contrast Enhanced Ultrasound Imaging for Assessment of Spinal Cord Blood Flow in Experimental Spinal Cord Injury

Reduced spinal cord blood flow (SCBF) (i.e., ischemia) plays a key role in traumatic spinal cord injury (SCI) pathophysiology and is accordingly an important target for neuroprotective therapies. Although several techniques have been described to assess SCBF, they all have significant limitations. To overcome the latter, we propose the use of real-time contrast enhanced ultrasound imaging (CEU). Here we describe the application of this technique in a rat contusion model of SCI. A jugular catheter is first implanted for the repeated injection of contrast agent, a sodium chloride solution of sulphur hexafluoride encapsulated microbubbles. The spine is then stabilized with a custom-made 3D-frame and the spinal cord dura mater is exposed by a laminectomy at ThIX-ThXII. The ultrasound probe is then positioned at the posterior aspect of the dura mater (coated with ultrasound gel). To assess baseline SCBF, a single intravenous injection (400 &#181;l) of contrast agent is applied to record its passage through the intact spinal cord microvasculature. A weight-drop device is subsequently used to generate a reproducible experimental contusion model of SCI. Contrast agent is re-injected 15 min following the injury to assess post-SCI SCBF changes. CEU allows for real time and in-vivo assessment of SCBF changes following SCI. In the uninjured animal, ultrasound imaging showed uneven blood flow along the intact spinal cord. Furthermore, 15 min post-SCI, there was critical ischemia at the level of the epicenter while SCBF remained preserved in the more remote intact areas. In the regions adjacent to the epicenter (both rostral and caudal), SCBF was significantly reduced. This corresponds to the previously described &#8220;ischemic penumbra zone&#8221;. This tool is of major interest for assessing the effects of therapies aimed at limiting ischemia and the resulting tissue necrosis subsequent to SCI.

Contrast Enhanced Ultrasound imaging is a reliable in-vivo tool for quantifying spinal cord blood flow in an experimental rat spinal cord injury model. This paper contains a comprehensive protocol for application of this technique in association with a contusion model of thoracic spinal cord injury.

Reduced spinal cord blood flow (SCBF) (i.e., ischemia) plays a key role in traumatic spinal cord injury (SCI) pathophysiology and is accordingly an ...

Simultaneous PET/MRI Imaging During Mouse Cerebral Hypoxia-ischemia

Dynamic changes in tissue water diffusion and glucose metabolism occur during and after hypoxia in cerebral hypoxia-ischemia reflecting a bioenergetics disturbance in affected cells. Diffusion weighted magnetic resonance imaging (MRI) identifies regions that are damaged, potentially irreversibly, by hypoxia-ischemia. Alterations in glucose utilization in the affected tissue may be detectable by positron emission tomography (PET) imaging of 2-deoxy-2-(18F)fluoro-&#7429;-glucose ([18F]FDG) uptake. Due to the rapid and variable nature of injury in this animal model, acquisition of both modes of data must be performed simultaneously in order to meaningfully correlate PET and MRI data. In addition, inter-animal variability in the hypoxic-ischemic injury due to vascular differences limits the ability to analyze multi-modal data and observe changes to a group-wise approach if data is not acquired simultaneously in individual subjects. The method presented here allows one to acquire both diffusion-weighted MRI and [18F]FDG uptake data in the same animal before, during, and after the hypoxic challenge in order to interrogate immediate physiological changes.

The method presented here uses simultaneous positron emission tomography and magnetic resonance imaging. In the cerebral hypoxia-ischemia model, dynamic changes in diffusion and glucose metabolism occur during and after injury. The evolving and irreproducible damage in this model necessitates simultaneous acquisition if meaningful multi-modal imaging data are to be acquired.

Dynamic changes in tissue water diffusion and glucose metabolism occur during and after hypoxia in cerebral hypoxia-ischemia reflecting a bioenergetics ...

An Organotypic High Throughput System for Characterization of Drug Sensitivity of Primary Multiple Myeloma Cells

In this work we describe a novel approach that combines ex vivo drug sensitivity assays and digital image analysis to estimate chemosensitivity and heterogeneity of patient-derived multiple myeloma (MM) cells. This approach consists in seeding primary MM cells freshly extracted from bone marrow aspirates into microfluidic chambers implemented in multi-well plates, each consisting of a reconstruction of the bone marrow microenvironment, including extracellular matrix (collagen or basement membrane matrix) and stroma (patient-derived mesenchymal stem cells) or human-derived endothelial cells (HUVECs). The chambers are drugged with different agents and concentrations, and are imaged sequentially for 96 hr through bright field microscopy, in a motorized microscope equipped with a digital camera. Digital image analysis software detects live and dead cells from presence or absence of membrane motion, and generates curves of change in viability as a function of drug concentration and exposure time. We use a computational model to determine the parameters of chemosensitivity of the tumor population to each drug, as well as the number of sub-populations present as a measure of tumor heterogeneity. These patient-tailored models can then be used to simulate therapeutic regimens and estimate clinical response.

We describe a high-throughput drug sensitivity assay for primary multiple myeloma cells. It consists of a reconstruction of the bone marrow microenvironment (including extracellular matrix and stroma) in multi-well plates, and a non-invasive method for longitudinal quantification of cell viability.

In this work we describe a novel approach that combines ex vivo drug sensitivity assays and digital image analysis to estimate chemosensitivity and ...

A Neonatal Mouse Spinal Cord Compression Injury Model

Spinal cord injury (SCI) typically causes devastating neurological deficits, particularly through damage to fibers descending from the brain to the spinal cord. A major current area of research is focused on the mechanisms of adaptive plasticity that underlie spontaneous or induced functional recovery following SCI. Spontaneous functional recovery is reported to be greater early in life, raising interesting questions about how adaptive plasticity changes as the spinal cord develops. To facilitate investigation of this dynamic, we have developed a SCI model in the neonatal mouse. The model has relevance for pediatric SCI, which is too little studied. Because neural plasticity in the adult involves some of the same mechanisms as neural plasticity in early life1, this model may potentially have some relevance also for adult SCI. Here we describe the entire procedure for generating a reproducible spinal cord compression (SCC) injury in the neonatal mouse as early as postnatal (P) day 1. SCC is achieved by performing a laminectomy at a given spinal level (here described at thoracic levels 9-11) and then using a modified Yasargil aneurysm mini-clip to rapidly compress and decompress the spinal cord. As previously described, the injured neonatal mice can be tested for behavioral deficits or sacrificed for ex vivo physiological analysis of synaptic connectivity using electrophysiological and high-throughput optical recording techniques1. Earlier and ongoing studies using behavioral and physiological assessment have demonstrated a dramatic, acute impairment of hindlimb motility followed by a complete functional recovery within 2 weeks, and the first evidence of changes in functional circuitry at the level of identified descending synaptic connections1.

This article describes a method for generating a reproducible spinal cord compression injury (SCI) in the neonatal mouse. The model provides an advantageous platform for studying mechanisms of adaptive plasticity that underlie spontaneous functional recovery.

Spinal cord injury (SCI) typically causes devastating neurological deficits, particularly through damage to fibers descending from the brain to the spinal ...

Evaluation of Coronary Flow Reserve After Myocardial Ischemia Reperfusion in Rats

Coronary artery disease is the leading cause of death worldwide. After an acute myocardial infarction, early and successful myocardial intervention via recanalization of the coronary artery is the most effective strategy for reducing the size of ischemic myocardium. The coronary microvasculature cannot be visualized and imaged&#160;in vivo, but there are several invasive and noninvasive techniques that can be used to assess parameters which depend directly on coronary microvascular function. The endothelial function after ischemia reperfusion can be assessed also at the level of the coronary circulation via the coronary flow reserve (CFR).&#160;In this study, peak velocity of left anterior descending (LAD) coronary arteries was measured in rats in vivo via Transthoracic Doppler Echocardiography during resting and stress challenge (induced by Dobutamine). A normal heart can increase its coronary blood flow up to four times above the resting values during stress induction. Following ischemia reperfusion, we found a significantly diminished CFR, which can be used as a marker of coronary microvascular dysfunction. CFR has opened a window on the importance of microvascular dysfunction and has been shown to predict cardiovascular risk independent of whether the severe obstructive disease is present.

Coronary flow reserve (CFR), is defined as the ratio of maximal coronary blood flow to the resting coronary blood flow. We present a protocol for evaluating CFR in rats via ultrasound, which offers the opportunity to predict cardiovascular risk factors in the absence of obstructive coronary disease.

Coronary artery disease is the leading cause of death worldwide. After an acute myocardial infarction, early and successful myocardial intervention via ...

Flow Cytometry Analysis of Immune Cell Subsets within the Murine Spleen, Bone Marrow, Lymph Nodes and Synovial Tissue in an Osteoarthritis Model

Osteoarthritis (OA) is one of the most prevalent musculoskeletal diseases, affecting patients suffering from pain and physical limitations. Recent evidence indicates a potential inflammatory component of the disease, with both T-cells and monocytes/macrophages potentially associated with the pathogenesis of OA. Further studies postulated an important role for subsets of both inflammatory cell lineages, such as Th1, Th2, Th17, and T-regulatory lymphocytes, and M1, M2, and synovium-tissue-resident macrophages. However, the interaction between the local synovial and systemic inflammatory cellular response and the structural changes in the joint is unknown. To fully understand how T-cells and monocytes/macrophages contribute towards OA, it is important to be able to quantitively identify these cells and their subsets simultaneously in synovial tissue, secondary lymphatic organs and systemically (the spleen and bone marrow). Nowadays, the different inflammatory cell subsets can be identified by a combination of cell-surface markers making multi-color flow cytometry a powerful technique in investigating these cellular processes. In this protocol, we describe detailed steps regarding the harvest of synovial tissue and secondary lymphatic organs as well as generation of single cell suspensions. Furthermore, we present both an extracellular staining assay to identify monocytes/macrophages and their subsets as well as an extra- and intra-cellular staining assay to identify T-cells and their subsets within the murine spleen, bone marrow, lymph nodes and synovial tissue. Each step of this protocol was optimized and tested, resulting in a highly reproducible assay that can be utilized for other surgical and non-surgical OA mouse models.

Here, we describe a detailed and reproducible flow cytometry protocol to identify monocyte/macrophage and T-cell subsets using both extra- and intracellular staining assays within the murine spleen, bone marrow, lymph nodes and synovial tissue, utilizing an established surgical model of murine osteoarthritis.