The authors thank all members of the Ito laboratory, especially K Ito and H Sato, and the Einstein Stem Cell Institute for comments and the Einstein Flow Cytometry and Analytical Imaging core facilities (funded by National Cancer Institute grant P30 CA013330) for help carrying out the experiments. K.I. is supported by grants from the National Institutes of Health (R01DK98263, R01DK115577, and R01DK100689) and the New York State Department of Health as Core Director of Einstein Single-Cell Genomics/Epigenomics (C029154). K.I. Ito is a Research Scholar of the Leukemia and Lymphoma Society.

All methods described here have been approved by the Institutional Animal Care and Use Committee (IACUC) of the Albert Einstein College of Medicine.
1. Preparation of Solutions
<ol>
	<li>Staining Buffer (phosphate-buffered saline (PBS) + 2% fetal bovine serum (FBS)): Add 10 mL of FBS in 500 mL of a sterile PBS solution. 
	NOTE: This solution can be stored at 4 &#176;C for at least one month in sterile condition. Before starting the following procedures, put an aliquot of this solution (50 mL) on ice.</li>
	<li>ACK (ammonium-chloride-potassium) lysing buffer: Place an aliquot of ACK lysing buffer (1 mL) on ice before starting the procedure. 
	NOTE: To prepare the same non-commercial buffer, dissolve 8.02 g of NH4Cl, 1 g of KHCO3 and 37.2 mg of Na2EDTA in 1 L of H2O. Adjust the pH to 7.2-7.4. Store for up to 6 months at room temperature.</li>
	<li>Culture medium: Add 50 ng/mL stem cell factor (SCF) and 50 ng/mL thrombopoietin (TPO) to serum-free medium for culture and expansion of hematopoietic cells (see Table of Material for commercial medium recommended).</li>
	<li>TMRM stock solution: Prepare TMRM (1 &#956;M) solution by dissolving 5 &#956;g of TMRM powder in 10 mL of ethanol. Store this solution at -20 &#176;C protected from the light.</li>
	<li>Verapamil stock solution: Prepare Verapamil (50 mM) solution by diluting 24 mg of Verapamil in 1 mL of ethanol. Store this solution at -20 &#176;C.</li>
	<li>FCCP stock solution: Prepare carbonilcyanide p-triflouromethoxyphenylhydrazone (FCCP) (1 M) solution by dissolving 254 mg in 1 mL of ethanol. Store this solution at -20 &#176;C protected from the light.</li>
</ol>
2. Bone Marrow Isolation
<ol>
	<li>Euthanize the mouse by CO2 inhalation following institutional guidelines and spray the mice with 70% ethanol. 
	NOTE: This step prevents contamination of the cells of interest without compromising experimental results.</li>
	<li>Using a pair of forceps and sharp scissors, make a small snip in the ventral skin of the mouse and stretch the skin.</li>
	<li>Extract the femur and tibia while taking care not to dislodge the heads of the femur as they contain a large amount of bone marrow cells. Place the removed bones in a 6-well plate filled with 1.5 mL of staining buffer. 
	NOTE: This procedure does not require sterile area.</li>
	<li>Remove the muscles from the bones and cut the ends of the bones allowing the exit of the bone marrow (Figure 1A). Place the cleaned bones in new wells with 1.5 mL of staining buffer. 
	NOTE: Muscles and other tissues must be carefully removed to avoid syringe clogging in the next step.</li>
	<li>Flush out the bone marrow using a 3 mL syringe with a 25 G needle. 
	NOTE: Continue to flush the bone marrow until the bone becomes white (Figure 1B).</li>
	<li>Collect all cells in a 1.5 mL tube, centrifuge for 5 min at 180 x g then discard the supernatant (Figure 1C).</li>
	<li>Resuspend the pellet in 300 &#956;L of ice cold ACK lysing buffer very carefully, put on ice for 1 min and immediately inactive lysis by adding 1 mL of staining buffer. Centrifuge for 5 min at 180 x g. 
	NOTE: The cells pellet appears white (Figure 1D). The total number of cells isolated is about 2-4 x 107.</li>
	<li>Resuspend the pellets in 1 mL of staining buffer and filter using a cell-strainer cap (12 x 75 mm2, 5 mL of capacity) with a 35 &#956;m nylon mesh incorporated to obtain mononuclear cells. After blocking, keep the sample on ice.</li>
</ol>
3. Immunostaining for Detection of HSC
<ol>
	<li>Prepare Lineage (Lin) cocktail. In 400 &#956;L of staining buffer, add 4 &#956;L of the following biotinilated antibodies against CD3e, CD4, CD8, B220, CD11b, Gr1, Ter119, CD19, Nk1.1, IgM and Il7Ra to obtain a final dilution 1:100.</li>
	<li>Prepare fluorophores conjugated-antibodies (Abs). In 400 &#956;L of staining buffer, add 4 &#956;L of the following Abs to obtain a final dilution 1:100. Streptavidin-Pacific Blue, Sca1-PE/Cy7, c-kit-APC/Cy7, CD48-APC, CD150-PerCP/Cy5.5 and CD34-FITC. Keep in ice, protected from light.</li>
	<li>Centrifuge the sample for 5 min at 180 x g, then discard the supernatant.</li>
	<li>Add 400 &#956;L of Lin cocktail solution to the cells pellet. Add 4 &#956;L of CD135-biotinilated Ab. Vortex quickly to mix and incubate for 30 min in ice.</li>
	<li>Wash the sample adding 3 mL of staining buffer, spin down for 5 min at 180 x g and discard the supernatant.</li>
	<li>Add 400 &#956;L of Abs solution. Vortex quickly to mix and incubate for 30 min on ice.</li>
	<li>Wash the samples with 3 mL of staining buffer, spin down for 5 min at 180 x g and discard the supernatant.</li>
</ol>
4. TMRM Staining
<ol>
	<li>Prepare TMRM staining solution. Add 2.2 &#956;L of TMRM stock solution and 1.1 &#956;L of Verapamil (2 nM and 50 &#956;M as final concentration, respectively) in 1.1 mL of serum-free medium for culture and expansion of hematopoietic cells (see Table of Material for commercial medium recommended) with TPO and SCF. 
	NOTE: This is the most important step of the protocol. Verapamil addition is necessary to block the efflux pumps which are highly expressed in the HSCs and can extrude TMRM.</li>
	<li>Resuspend the bone marrow in 1 mL of TMRM staining solution, vortex quickly and incubate for 1 h at 37 &#176;C. 
	NOTE: TMRM staining must not be washed out. PE-dedicated compensation control is also resuspended in 100 &#956;L of TMRM staining solution, and subjected to incubation for 1 h at 37 &#176;C after quick vortex.</li>
	<li>Filter the sample using a cell-strainer cap (12 x 75 mm2, 5 mL of capacity) with a 35 &#956;m nylon mesh incorporated to avoid clogging of the flow cytometer. 
	NOTE: TMRM staining increases the possibility of clog formation in the sample. Filtration of the sample just before flow assays is recommended.</li>
	<li>Add 1 &#956;L of 4&#8217;,6-diamidino-2-phenylindole (DAPI) to exclude dead cells by flow cytometry.</li>
</ol>
5. Acquisition by Flow Cytometer
<ol>
	<li>Run bone marrow sample and acquire at least 1 x 106 events.</li>
	<li>Set up the gating strategy to identify the different hematopoietic populations (Figure 2).
	<ol>
		<li>Display live bone marrow mono-nuclear cells (BM-MNCs), DAPI&#8722; fraction, in plot for Pacific Blue to identify CD135&#8722;Lin&#8722; (Lin&#8722;) and Lin+ fractions.</li>
		<li>Plot Lin&#8722; fraction for APC/Cy7 (c-kit) versus PE/Cy7 (Sca-1) to identify multipotent progenitors (MPP) fraction, as c-kit+ and Sca-1+.</li>
		<li>Plot MPP fraction for APC (CD48) versus PerCP/Cy5.5 (CD150) to identify HSC fraction, as CD150+ and CD48&#8722;.</li>
		<li>Display HSC fraction for FITC (CD34) to divide CD34&#8722;-HSC and CD34+-HSC.</li>
	</ol>
	</li>
	<li>Acquire the TMRM intensity (PE channel) in each population.</li>
	<li>After acquisition, add to the sample 1 &#956;L of FCCP to obtain the final concentration of 1 mM and incubate at 37 &#176;C for 5 min, then acquire 1 x 106 events. 
	NOTE: FCCP is a mitochondrial uncoupler which is used to dissipate the &#916;&#936;m. It is used as experimental control to confirm that TMRM staining works correctly. After the administration of FCCP, the TMRM intensity should drastically be decreased (Figure 3A).</li>
	<li>Analyze data normalizing the average intensity of PE of each population by the intensity of PE of all BM-MNCs.</li>
</ol>

<ol>
	<li>Weissman, I. L., Anderson, D. J., Gage, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stem+and+progenitor+cells:+origins,+phenotypes,+lineage+commitments,+and+transdifferentiations.">Stem and progenitor cells: origins, phenotypes, lineage commitments, and transdifferentiations.</a> Annual Review of Cell and Developmental Biology. 17, 387-403 (2001).</li><li>Morrison, S. J., Shah, N. M., Anderson, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulatory+mechanisms+in+stem+cell+biology.">Regulatory mechanisms in stem cell biology.</a> Cell. 88 (3), 287-298 (1997).</li><li>Wilson, A., 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=Hematopoietic+stem+cells+reversibly+switch+from+dormancy+to+self-renewal+during+homeostasis+and+repair.">Hematopoietic stem cells reversibly switch from dormancy to self-renewal during homeostasis and repair.</a> Cell. 135 (6), 1118-1129 (2008).</li><li>Morrison, S. J., Scadden, D. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+bone+marrow+niche+for+haematopoietic+stem+cells.">The bone marrow niche for haematopoietic stem cells.</a> Nature. 505 (7483), 327-334 (2014).</li><li>Frenette, P. S., Pinho, S., Lucas, D., Scheiermann, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mesenchymal+stem+cell:+keystone+of+the+hematopoietic+stem+cell+niche+and+a+stepping-stone+for+regenerative+medicine.">Mesenchymal stem cell: keystone of the hematopoietic stem cell niche and a stepping-stone for regenerative medicine.</a> Annual Review of Immunology. 31, 285-316 (2013).</li><li>Ito, K., Bonora, M., Ito, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Metabolism+as+master+of+hematopoietic+stem+cell+fate.">Metabolism as master of hematopoietic stem cell fate.</a> International Journal of Hematology. 109 (1), 18-27 (2019).</li><li>Ito, K., 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=Self-renewal+of+a+purified+Tie2++hematopoietic+stem+cell+population+relies+on+mitochondrial+clearance.">Self-renewal of a purified Tie2+ hematopoietic stem cell population relies on mitochondrial clearance.</a> Science. 354 (6316), 1156-1160 (2016).</li><li>Bonora, 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=ATP+synthesis+and+storage.">ATP synthesis and storage.</a> Purinergic Signal. 8 (3), 343-357 (2012).</li><li>Walker, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+regulation+of+catalysis+in+ATP+synthase.">The regulation of catalysis in ATP synthase.</a> Current Opinion in Structural Biology. 4 (6), 912-918 (1994).</li><li>Scaduto, R. C., Grotyohann, L. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measurement+of+mitochondrial+membrane+potential+using+fluorescent+rhodamine+derivatives.">Measurement of mitochondrial membrane potential using fluorescent rhodamine derivatives.</a> Biophysical Journal. 76, 469-477 (1999).</li><li>Bonora, M., Ito, K., Morganti, C., Pinton, P., Ito, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Membrane-potential+compensation+reveals+mitochondrial+volume+expansion+during+HSC+commitment.">Membrane-potential compensation reveals mitochondrial volume expansion during HSC commitment.</a> Experimental Hematology. 68, 30-37 (2018).</li><li>Goodell, M. A., 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=Dye+efflux+studies+suggest+that+hematopoietic+stem+cells+expressing+low+or+undetectable+levels+of+CD34+antigen+exist+in+multiple+species.">Dye efflux studies suggest that hematopoietic stem cells expressing low or undetectable levels of CD34 antigen exist in multiple species.</a> Nature Medicine. 3 (12), 1337-1345 (1997).</li><li>Spangrude, G. J., Johnson, G. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Resting+and+activated+subsets+of+mouse+multipotent+hematopoietic+stem+cells.">Resting and activated subsets of mouse multipotent hematopoietic stem cells.</a> Proceedings of the National Academy of Sciences of the United States of America. 87 (19), 7433-7437 (1990).</li><li>Scharenberg, C. W., Harkey, M. A., Torok-Storb, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ABCG2+transporter+is+an+efficient+Hoechst+33342+efflux+pump+and+is+preferentially+expressed+by+immature+human+hematopoietic+progenitors.">The ABCG2 transporter is an efficient Hoechst 33342 efflux pump and is preferentially expressed by immature human hematopoietic progenitors.</a> Blood. 99 (2), 507-512 (2002).</li><li>Zhou, 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=The+ABC+transporter+Bcrp1/ABCG2+is+expressed+in+a+wide+variety+of+stem+cells+and+is+a+molecular+determinant+of+the+side-population+phenotype.">The ABC transporter Bcrp1/ABCG2 is expressed in a wide variety of stem cells and is a molecular determinant of the side-population phenotype.</a> Nature Medicine. 7 (9), 1028-1034 (2001).</li><li>Simsek, T., 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=The+distinct+metabolic+profile+of+hematopoietic+stem+cells+reflects+their+location+in+a+hypoxic+niche.">The distinct metabolic profile of hematopoietic stem cells reflects their location in a hypoxic niche.</a> Cell Stem Cell. 7 (3), 380-390 (2010).</li><li>Vannini, N., 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=Specification+of+haematopoietic+stem+cell+fate+via+modulation+of+mitochondrial+activity.">Specification of haematopoietic stem cell fate via modulation of mitochondrial activity.</a> Nature Communications. 7, 13125 (2016).</li><li>Xiao, N., 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=Hematopoietic+stem+cells+lacking+Ott1+display+aspects+associated+with+aging+and+are+unable+to+maintain+quiescence+during+proliferative+stress.">Hematopoietic stem cells lacking Ott1 display aspects associated with aging and are unable to maintain quiescence during proliferative stress.</a> Blood. 119 (21), 4898-4907 (2012).</li><li>de Almeida, M. J., Luchsinger, L. L., Corrigan, D. J., Williams, L. J., Snoeck, H. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dye-Independent+Methods+Reveal+Elevated+Mitochondrial+Mass+in+Hematopoietic+Stem+Cells.">Dye-Independent Methods Reveal Elevated Mitochondrial Mass in Hematopoietic Stem Cells.</a> Cell Stem Cell. 21 (6), 725-729 (2017).</li><li>Hall, A. M., Rhodes, G. J., Sandoval, R. M., Corridon, P. R., Molitoris, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+multiphoton+imaging+of+mitochondrial+structure+and+function+during+acute+kidney+injury.">In vivo multiphoton imaging of mitochondrial structure and function during acute kidney injury.</a> Kidney International. 83 (1), 72-83 (2013).</li><li>Oguro, H., Ding, L., Morrison, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SLAM+family+markers+resolve+functionally+distinct+subpopulations+of+hematopoietic+stem+cells+and+multipotent+progenitors.">SLAM family markers resolve functionally distinct subpopulations of hematopoietic stem cells and multipotent progenitors.</a> Cell Stem Cell. 13 (1), 102-116 (2013).</li><li>Nicolli, A., Basso, E., Petronilli, V., Wenger, R. M., Bernardi, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interactions+of+cyclophilin+with+the+mitochondrial+inner+membrane+and+regulation+of+the+permeability+transition+pore,+and+cyclosporin+A-sensitive+channel.">Interactions of cyclophilin with the mitochondrial inner membrane and regulation of the permeability transition pore, and cyclosporin A-sensitive channel.</a> The Journal of Biological Chemistry. 271 (4), 2185-2192 (1996).</li><li>Vannini, N., 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=The+NAD-Booster+Nicotinamide+Riboside+Potently+Stimulates+Hematopoiesis+through+Increased+Mitochondrial+Clearance.">The NAD-Booster Nicotinamide Riboside Potently Stimulates Hematopoiesis through Increased Mitochondrial Clearance.</a> Cell Stem Cell. 24 (3), 405-418 (2019).</li></ol>

The authors have nothing to disclose.

Mitochondrial membrane potential measurement is a cornerstone of the analysis and assessment of mitochondria, which are critical to the metabolic state of the cell. Here, we describe a protocol for the analysis of &#916;&#936;m by TMRM staining. TMRM is a cell-permeant fluorescent dye which accumulates in active mitochondria due to &#916;&#936;m, and its respective levels remain in equilibrium between the extracellular, cytoplasmic and mitochondrial compartments10. This protocol can be adapted for...

Hematopoietic stem cells (HSCs) are self-renewing, multi-potent, and capable of giving rise to all the cells of the blood1,2. Cellular metabolism is a key regulator of HSC maintenance, along with transcriptional factors, intrinsic signals and the microenvironment3,4,5. The proper control of mitochondrial function and quality is therefore critical to HSC maintenance6,7.
Mitochondrial membrane potential (&#916;&#936;m) is a key parameter in the assessment of mitochondria as it directly reflects their functionality, which derives from the equilibrium of proton pumping activity in the electron transport chain and the proton flow through F1/FO ATP synthase. These are both required (depending on gene expression and substrate availability) for the oxygen-dependent phosphorylation of ADP to ATP8,9. Taking advantage of the electronegativity of the mitochondrial compartment, various potentiometric dyes have been developed to measure &#916;&#936;m. One of them is tetramethylrhodamine methyl ester perchlorate (TMRM), which has been extensively used to measure &#916;&#936;m by flow cytometry in a variety of cells10, including hematopoietic stem and progenitor cells11. &#160;
Mitochondrial dyes must be used with some caution in HSCs, however, because the high activity of the xenobiotic efflux pumps of these cells can result in dye extrusion12. Indeed, the extrusion of mitochondrial dyes such as Rhodamine 123 has allowed researchers to isolate HSCs13 or identify HSC &#8220;side populations&#8221; by exploiting the differential extrusion of the dyes Hoechst Blue and Hoechst Red14,15. It has also been shown that Fumitremorgin C, a specific blocker of the ATP-binding cassette sub-family G member 2 (ABCG2) transporter, does not affect the staining pattern of MitoTracker in HSPCs16. After the publication of these results, multiple studies were performed using mitochondrial dyes in the absence of xenobiotic efflux pump inhibitors, leading to the widespread impression that HSCs have only a small number of mitochondria with low &#916;&#936;m16,17,18.
Recently, it was demonstrated, however, that Verapamil, a wide spectrum inhibitor of efflux pumps, significantly modifies the staining pattern of the mitochondrial dye MitoTracker Green19. This discrepancy is likely due to the fact that Fumitremorgin C is highly selective for Abcg2, while HSCs also express other transporters such as Abcb1a (which is only weakly sensitive to Fumitremorgin C)19. We have also reported that other mitochondrial dyes, such as TMRM, Nonyl acridine orange, and Mitotracker Orange (MTO) exhibit the same patterns as Mitotracker Green. More importantly, we have observed that the flow cytometric patterns of HSPCs reflect their &#916;&#936;m in addition to mitochondrial mass11.
The intake of TMRM dye strictly depends on the negative charge of mitochondria, but the resulting accumulation of dye is in constant balance between its intake and clearance by efflux pumps20. The difference in xenobiotic efflux pump expression between HSCs and mature cell populations affects this balance and can lead to biased results. The use of dedicated inhibitors such as Verapamil should be considered in the analysis of &#916;&#936;m by potentiometric dyes. Here we describe a modified protocol for accurate &#916;&#936;m measurement by TMRM-based flow cytometry which corrects for xenobiotic transporter activity through the use of dedicated inhibitors.

<table>
	<tbody>
		<tr>
			<td>ACK lysing buffer</td>
			<td>Life Technologies</td>
			<td>A1049201</td>
			<td></td>
		</tr>
		<tr>
			<td>B220-biotin</td>
			<td>BD Bioscience</td>
			<td>553086</td>
			<td></td>
		</tr>
		<tr>
			<td>CD3e-biotin</td>
			<td>Life Technologies</td>
			<td>13-0031-85</td>
			<td></td>
		</tr>
		<tr>
			<td>CD4-biotin</td>
			<td>Fischer Scientific</td>
			<td>BDB553782</td>
			<td></td>
		</tr>
		<tr>
			<td>CD8-biotin</td>
			<td>Life Technologies</td>
			<td>13-0081-85</td>
			<td></td>
		</tr>
		<tr>
			<td>CD11b-biotin</td>
			<td>BD Bioscience</td>
			<td>553309</td>
			<td></td>
		</tr>
		<tr>
			<td>CD19-biotin</td>
			<td>BD Bioscience</td>
			<td>553784</td>
			<td></td>
		</tr>
		<tr>
			<td>CD34-FITC</td>
			<td>eBioscience</td>
			<td>11-0341-85</td>
			<td></td>
		</tr>
		<tr>
			<td>CD48-APC</td>
			<td>eBioscience</td>
			<td>17-0481-82</td>
			<td></td>
		</tr>
		<tr>
			<td>CD135-biotin</td>
			<td>eBioscience</td>
			<td>13-1351-82</td>
			<td></td>
		</tr>
		<tr>
			<td>CD150-PerCP/Cy5.5&#160;</td>
			<td>Biolegend</td>
			<td>115922</td>
			<td></td>
		</tr>
		<tr>
			<td>c-kit-APC/Cy7</td>
			<td>Biolegend</td>
			<td>105826</td>
			<td></td>
		</tr>
		<tr>
			<td>Cyclosporin H</td>
			<td>Millipore Sigma</td>
			<td>SML1575-1MG</td>
			<td></td>
		</tr>
		<tr>
			<td>DAPI solution (1mg/mL)</td>
			<td>Life Technologies</td>
			<td>62248</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum (FBS)</td>
			<td>Denville</td>
			<td>FB5001-H</td>
			<td></td>
		</tr>
		<tr>
			<td>FCCP</td>
			<td>Millipore Sigma</td>
			<td>C2920-10MG</td>
			<td></td>
		</tr>
		<tr>
			<td>Gr1-biotin</td>
			<td>Biolegend</td>
			<td>108404</td>
			<td></td>
		</tr>
		<tr>
			<td>IgM-biotin</td>
			<td>Life Technologies</td>
			<td>13-5790-85</td>
			<td></td>
		</tr>
		<tr>
			<td>Il7R&#945;-biotin</td>
			<td>eBioscience</td>
			<td>13-1271-85</td>
			<td></td>
		</tr>
		<tr>
			<td>Nk1.1-biotin</td>
			<td>Fischer Scientific</td>
			<td>BDB553163</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate buffered saline (PBS)</td>
			<td>Life Technologies</td>
			<td>10010023</td>
			<td></td>
		</tr>
		<tr>
			<td>Sca-1-PE/Cy7</td>
			<td>eBioscience</td>
			<td>25-5981-81</td>
			<td></td>
		</tr>
		<tr>
			<td>SCF murine</td>
			<td>PEPROTECH</td>
			<td>250-03-10UG</td>
			<td></td>
		</tr>
		<tr>
			<td>StemSpan SFEM medium</td>
			<td>STEMCELL technologies</td>
			<td>9605</td>
			<td></td>
		</tr>
		<tr>
			<td>Streptavidin-Pacific Blue</td>
			<td>eBioscience</td>
			<td>48-4317-82</td>
			<td></td>
		</tr>
		<tr>
			<td>Ter119-biotin</td>
			<td>Fischer Scientific</td>
			<td>BDB553672</td>
			<td></td>
		</tr>
		<tr>
			<td>TMRM</td>
			<td>Millipore Sigma</td>
			<td>T5428-25MG</td>
			<td></td>
		</tr>
		<tr>
			<td>TPO</td>
			<td>PEPROTECH</td>
			<td>315-14-10UG</td>
			<td></td>
		</tr>
		<tr>
			<td>Verapamil hydrochloride</td>
			<td>Millipore Sigma</td>
			<td>V4629-1G</td>
			<td></td>
		</tr>
	</tbody>
</table>

improving the accuracy of flow cytometric assessment of mitochondrial membrane potential in hematopoietic stem and progenitor cells through the inhibition of efflux pumps

As cellular metabolism is a key regulator of hematopoietic stem cell (HSC) self-renewal, the various roles played by the mitochondria in hematopoietic homeostasis have been extensively studied by HSC researchers. Mitochondrial activity levels are reflected in their membrane potentials (&#916;&#936;m), which can be measured by cell-permeant cationic dyes such as TMRM (tetramethylrhodamine, methyl ester). The ability of efflux pumps to extrude these dyes from cells can limit their usefulness, however. The resulting measurement bias is particularly critical when assessing HSCs, as xenobiotic transporters exhibit higher levels of expression and activity in HSCs than in differentiated cells. Here, we describe a protocol utilizing Verapamil, an efflux pump inhibitor, to accurately measure &#916;&#936;m across multiple bone marrow populations. The resulting inhibition of pump activity is shown to increase TMRM intensity in hematopoietic stem and progenitor cells (HSPCs), while leaving it relatively unchanged in mature fractions. This highlights the close attention to dye-efflux activity that is required when &#916;&#936;m-dependent dyes are used, and as written and visualized, this protocol can be used to accurately compare either different populations within the bone marrow, or the same population across different experimental models.

The protocol described above enables the easy isolation of BM-MNCs from a mouse model. Figure 1 summarizes the main steps of the protocol: bone isolation, flushing out of the bone marrow, red blood cell lysis, and antibody staining followed by TMRM staining to measure mitochondrial membrane potential in a specific hematopoietic population.
BM-MNCs contain several cell populations, including HSCs. The antibody cocktails used in this protocol are well-established in...

Watch this Scientific Journal Video about Improving the Accuracy of Flow Cytometric Assessment of Mitochondrial Membrane Potential in Hematopoietic Stem and Progenitor Cells Through the Inhibition of 

Improving the Accuracy of Flow Cytometric Assessment of Mitochondrial Membrane Potential in Hematopoietic Stem and Progenitor Cells Through the Inhibition of Efflux Pumps

Xenobiotic efflux pumps are highly active in hematopoietic stem and progenitor cells (HSPCs) and cause extrusion of TMRM, a mitochondrial membrane potential fluorescent dye. Here, we present a protocol to accurately measure mitochondrial membrane potential in HSPCs by TMRM in the presence of Verapamil, an efflux pump inhibitor.

As cellular metabolism is a key regulator of hematopoietic stem cell (HSC) self-renewal, the various roles played by the mitochondria in hematopoietic ...

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7.7K Views.  Albert Einstein College of Medicine. Xenobiotic efflux pumps are highly active in hematopoietic stem and progenitor cells (HSPCs) and cause extrusion of TMRM, a mitochondrial membrane potential fluorescent dye. Here, we present a protocol to accurately measure mitochondrial membrane potential in HSPCs by TMRM in the presence of Verapamil, an efflux pump inhibitor.

Video: Improving the Accuracy of Flow Cytometric Assessment of Mitochondrial Membrane Potential in Hematopoietic Stem and Progenitor Cells Through the Inhibition of Efflux Pumps

Isolation and Analysis of Hematopoietic Stem Cells from the Placenta

Hematopoietic stem cells (HSCs) have the ability to self-renew and generate all cell types of the blood lineages throughout the lifetime of an individual. All HSCs emerge during embryonic development, after which their pool size is maintained by self-renewing cell divisions. Identifying the anatomical origin of HSCs and the critical developmental events regulating the process of HSC development has been complicated as many anatomical sites participate during fetal hematopoiesis. Recently, we identified the placenta as a major hematopoietic organ where HSCs are generated and expanded in unique microenvironmental niches (Gekas, et al 2005, Rhodes, et al 2008). Consequently, the placenta is an important source of HSCs during their emergence and initial expansion.
In this article, we show dissection techniques for the isolation of murine placenta from E10.5 and E12.5 embryos, corresponding to the developmental stages of initiation of HSCs and the peak in the size of the HSC pool in the placenta, respectively. In addition, we present an optimized protocol for enzymatic and mechanical dissociation of placental tissue into single-cell suspension for use in flow cytometry or functional assays. We have found that use of collagenase for single-cell suspension of placenta gives sufficient yields of HSCs. An important factor affecting HSC yield from the placenta is the degree of mechanical dissociation prior to, and duration of, enzymatic treatment.
We also provide a protocol for the preparation of fixed-frozen placental tissue sections for the visualization of developing HSCs by immunohistochemistry in their precise cellular niches. As hematopoietic specific antigens are not preserved during preparation of paraffin embedded sections, we routinely use fixed frozen sections for localizing placental HSCs and progenitors.

We have identified the placenta as a major hematopoietic organ during development. We found that hematopoietic stem cells (HSCs) are both generated and expanded in the placenta in unique microenvironmental niches. Here, we describe experimental techniques required for isolation and visualization of HSCs in the mouse placenta.

Hematopoietic stem cells (HSCs) have the ability to self-renew and generate all cell types of the blood lineages throughout the lifetime of an individual. ...

Lentiviral-mediated Knockdown During Ex Vivo Erythropoiesis of Human Hematopoietic Stem Cells

Erythropoiesis is a commonly used model system to study cell differentiation. During erythropoiesis, pluripotent adult human hematopoietic stem cells (HSCs) differentiate into oligopotent progenitors, committed precursors and mature red blood cells 1. This process is regulated for a large part at the level of gene expression, whereby specific transcription factors activate lineage-specific genes while concomitantly repressing genes that are specific to other cell types 2. Studies on transcription factors regulating erythropoiesis are often performed using human and murine cell lines that represent, to some extent, erythroid cells at given stages of differentiation 3-5. However transformed cell lines can only partially mimic erythroid cells and most importantly they do not allow one to comprehensibly study the dynamic changes that occur as cells progress through many stages towards their final erythroid fate. Therefore, a current challenge remains the development of a protocol to obtain relatively homogenous populations of primary HSCs and erythroid cells at various stages of differentiation in quantities that are sufficient to perform genomics and proteomics experiments.
Here we describe an ex vivo cell culture protocol to induce erythroid differentiation from human hematopoietic stem/progenitor cells that have been isolated from either cord blood, bone marrow, or adult peripheral blood mobilized with G-CSF (leukapheresis). This culture system, initially developed by the Douay laboratory 6, uses cytokines and co-culture on mesenchymal cells to mimic the bone marrow microenvironment. Using this ex vivo differentiation protocol, we observe a strong amplification of erythroid progenitors, an induction of differentiation exclusively towards the erythroid lineage and a complete maturation to the stage of enucleated red blood cells. Thus, this system provides an opportunity to study the molecular mechanism of transcriptional regulation as hematopoietic stem cells progress along the erythroid lineage. 
Studying erythropoiesis at the transcriptional level also requires the ability to over-express or knockdown specific factors in primary erythroid cells. For this purpose, we use a lentivirus-mediated gene delivery system that allows for the efficient infection of both dividing and non-dividing cells 7. Here we show that we are able to efficiently knockdown the transcription factor TAL1 in primary human erythroid cells. In addition, GFP expression demonstrates an efficiency of lentiviral infection close to 90%. Thus, our protocol provides a highly useful system for characterization of the regulatory network of transcription factors that control erythropoiesis.

Lentiviral-mediated Knockdown During Ex Vivo Erythropoiesis of Human Hematopoietic Stem Cells

An ex vivo protocol to generate mature human red blood cells from hematopoietic stem/progenitors is described. Additionally we describe an efficient lentiviral-delivery method to knockdown the transcription factor TAL1 in primary erythroid cells. The efficiency of lentivirus mediated gene delivery is demonstrated using GFP expressing viruses.

Erythropoiesis is a commonly used model system to study cell differentiation. During erythropoiesis, pluripotent adult human hematopoietic stem cells ...

In Vivo 4-Dimensional Tracking of Hematopoietic Stem and Progenitor Cells in Adult Mouse Calvarial Bone Marrow

Through a delicate balance between quiescence and proliferation, self renewal and production of differentiated progeny, hematopoietic stem cells (HSCs) maintain the turnover of all mature blood cell lineages. The coordination of the complex signals leading to specific HSC fates relies upon the interaction between HSCs and the intricate bone marrow microenvironment, which is still poorly understood[1-2].
We describe how by combining a newly developed specimen holder for stable animal positioning with multi-step confocal and two-photon in vivo imaging techniques, it is possible to obtain high-resolution 3D stacks containing HSPCs and their surrounding niches and to monitor them over time through multi-point time-lapse imaging. High definition imaging allows detecting ex vivo labeled hematopoietic stem and progenitor cells (HSPCs) residing within the bone marrow. Moreover, multi-point time-lapse 3D imaging, obtained with faster acquisition settings, provides accurate information about HSPC movement and the reciprocal interactions between HSPCs and stroma cells.
Tracking of HSPCs in relation to GFP positive osteoblastic cells is shown as an exemplary application of this method. This technique can be utilized to track any appropriately labeled hematopoietic or stromal cell of interest within the mouse calvarium bone marrow space.

In Vivo 4-Dimensional Tracking of Hematopoietic Stem and Progenitor Cells in Adult Mouse Calvarial Bone Marrow

The nature of the interactions between hematopoietic stem and progenitor cells (HSPCs) and bone marrow niches is poorly understood. Custom hardware modifications and a multi-step acquisition protocol allow the use of two-photon and confocal microscopy to image ex vivo labeled HSPCs homed within bone marrow areas, tracking interactions and movement.

Through a delicate balance between quiescence and proliferation, self renewal and production of differentiated progeny, hematopoietic stem cells (HSCs) ...

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Hematopoietic stem cells (HSCs) are used clinically for transplantation treatment to rebuild a patient&#39;s hematopoietic system in many diseases such as leukemia and lymphoma. Elucidating the mechanisms controlling HSCs self-renewal and differentiation is important for application of HSCs for research and clinical uses. However, it is not possible to obtain large quantity of HSCs due to their inability to proliferate in vitro. To overcome this hurdle, we used a mouse bone marrow derived cell line, the EML (Erythroid, Myeloid, and Lymphocytic) cell line, as a model system for this study.
RNA-sequencing (RNA-Seq) has been increasingly used to replace microarray for gene expression studies. We report here a detailed method of using RNA-Seq technology to investigate the potential key factors in regulation of EML cell self-renewal and differentiation. The protocol provided in this paper is divided into three parts. The first part explains how to culture EML cells and separate Lin-CD34+ and Lin-CD34- cells. The second part of the protocol offers detailed procedures for total RNA preparation and the subsequent library construction for high-throughput sequencing. The last part describes the method for RNA-Seq data analysis and explains how to use the data to identify differentially expressed transcription factors between Lin-CD34+ and Lin-CD34- cells. The most significantly differentially expressed transcription factors were identified to be the potential key regulators controlling EML cell self-renewal and differentiation. In the discussion section of this paper, we highlight the key steps for successful performance of this experiment.
In summary, this paper offers a method of using RNA-Seq technology to identify potential regulators of self-renewal and differentiation in EML cells. The key factors identified are subjected to downstream functional analysis in vitro and in vivo.

RNA-sequencing and bioinformatics analyses were used to identify significantly and differentially expressed transcription factors in Lin-CD34+ and Lin-CD34- subpopulations of mouse EMLcells. These transcription factors might play important roles in determining the switch between self-renewing Lin-CD34+ and partially differentiated Lin-CD34- cells.

Hematopoietic stem cells (HSCs) are used clinically for transplantation treatment to rebuild a patient&#39;s hematopoietic system in many diseases such as ...

Simultaneous Measurement of Mitochondrial Calcium and Mitochondrial Membrane Potential in Live Cells by Fluorescent Microscopy

Apart from their essential role in generating ATP, mitochondria also act as local calcium (Ca2+) buffers to tightly regulate intracellular Ca2+ concentration. To do this, mitochondria utilize the electrochemical potential across their inner membrane (&#916;&#936;m) to sequester Ca2+. The influx of Ca2+ into the mitochondria stimulates three rate-limiting dehydrogenases of the citric acid cycle, increasing electron transfer through the oxidative phosphorylation (OXPHOS) complexes. This stimulation maintains &#916;&#936;m, which is temporarily dissipated as the positive calcium ions cross the mitochondrial inner membrane into the mitochondrial matrix.
We describe here a method for simultaneously measuring mitochondria Ca2+ uptake and &#916;&#936;m in live cells using confocal microscopy. By permeabilizing the cells, mitochondrial Ca2+ can be measured using the fluorescent Ca2+ indicator Fluo-4, AM, with measurement of &#916;&#936;m using the fluorescent dye tetramethylrhodamine, methyl ester, perchlorate (TMRM). The benefit of this system is that there is very little spectral overlap between the fluorescent dyes, allowing accurate measurement of mitochondrial Ca2+ and &#916;&#936;m simultaneously. Using the sequential addition of Ca2+ aliquots, mitochondrial Ca2+ uptake can be monitored, and the concentration at which Ca2+ induces mitochondrial membrane permeability transition and the loss of &#916;&#936;m determined.

Mitochondria can utilize the electrochemical potential across their inner membrane (&#916;&#936;m) to sequester calcium (Ca2+), allowing them to shape cytosolic Ca2+ signaling within the cell. We describe a method for simultaneously measuring mitochondria Ca2+ uptake and &#916;&#936;m in live cells using fluorescent dyes and confocal microscopy.

Apart from their essential role in generating ATP, mitochondria also act as local calcium (Ca2+) buffers to tightly regulate intracellular Ca2+ ...

Measurement of Mitochondrial Mass and Membrane Potential in Hematopoietic Stem Cells and T-cells by Flow Cytometry

A fine balance of quiescence, self-renewal, and differentiation is key to preserve the hematopoietic stem cell (HSC) pool and maintain lifelong production of all mature blood cells. In recent years cellular metabolism has emerged as a crucial regulator of HSC function and fate. We have previously demonstrated that modulation of mitochondrial metabolism influences HSC fate. Specifically, by chemically uncoupling the electron transport chain we were able to maintain HSC function in culture conditions that normally induce rapid differentiation. However, limiting HSC numbers often precludes the use of standard assays to measure HSC metabolism and therefore predict their function. Here, we report a simple flow cytometry assay that allows reliable measurement of mitochondrial membrane potential and mitochondrial mass in scarce cells such as HSCs. We discuss the isolation of HSCs from mouse bone marrow and measurement of mitochondrial mass and membrane potential post ex vivo culture. As an example, we show the modulation of these parameters in HSCs via treatment with a metabolic modulator. Moreover, we extend the application of this methodology on human peripheral blood-derived T cells and human tumor infiltrating lymphocytes (TILs), showing dramatic differences in their mitochondrial profiles, possibly reflecting different T cell functionality. We believe this assay can be employed in screenings to identify modulators of mitochondrial metabolism in various cell types in different contexts.

Here we describe a reliable method to measure mitochondrial mass and membrane potential in ex vivo cultured hematopoietic stem cells and T cells.

A fine balance of quiescence, self-renewal, and differentiation is key to preserve the hematopoietic stem cell (HSC) pool and maintain lifelong production ...

Assessment of Cellular Bioenergetics in Mouse Hematopoietic Stem and Primitive Progenitor Cells using the Extracellular Flux Analyzer

Under steady state, hematopoietic stem cells (HSCs) remain largely quiescent and are believed to be predominantly reliant on glycolysis to meet their energetic needs. However, under stress conditions such as infection or blood loss, HSCs become proliferative and rapidly produce downstream progenitor cells, which in turn further differentiate, ultimately producing mature blood cells. During this transition and differentiation process, HSCs exit from quiescence and rapidly undergo a metabolic switch from glycolysis to oxidative phosphorylation (OxPHOS). Various stress conditions, such as aging, cancer, diabetes, and obesity, can negatively impact mitochondrial function and thus can alter the metabolic reprogramming and differentiation of HSCs and progenitors during hematopoiesis. Valuable insights into glycolytic and mitochondrial functions of HSCs and progenitors under normal and stress conditions can be gained through the assessment of their extracellular acidification rate (ECAR) and oxygen consumption rate (OCR), which are indicators of cellular glycolysis and mitochondrial respiration, respectively. 
Here, a detailed protocol is provided to measure ECAR and OCR in mouse bone marrow-derived lineage-negative cell populations, which include both hematopoietic stem and primitive progenitor cells (HSPCs), using the extracellular flux analyzer. This protocol describes approaches to isolate lineage-negative cells from mouse bone marrow, explains optimization of cell seeding density and concentrations of 2-deoxy-D-glucose (2-DG, a glucose analog that inhibits glycolysis) and various OxPHOS-targeted drugs (oligomycin, FCCP, rotenone, and antimycin A) used in these assays, and describes drug treatment strategies. Key parameters of glycolytic flux, such as glycolysis, glycolytic capacity, and glycolytic reserve, and OxPHOS parameters, such as basal respiration, maximal respiration, proton leak, ATP production, spare respiratory capacity, and coupling efficiency, can be measured in these assays. This protocol allows ECAR and OCR measurements on non-adherent HSPCs and can be generalized to optimize analysis conditions for any type of suspension cells.

The method presented here summarizes optimized protocols for assessing cellular bioenergetics in non-adherent mouse hematopoietic stem and primitive progenitor cells (HSPCs) using the extracellular flux analyzer to measure the extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) of HSPCs in real time.

Under steady state, hematopoietic stem cells (HSCs) remain largely quiescent and are believed to be predominantly reliant on glycolysis to meet their ...

Functional Assessment of Kinesin-7 CENP-E in Spermatocytes Using In Vivo Inhibition, Immunofluorescence and Flow Cytometry

In eukaryotes, meiosis is essential for genome stability and genetic diversity in sexual reproduction. Experimental analyses of spermatocytes in testes are critical for the investigations of spindle assembly and chromosome segregation in male meiotic division. The mouse spermatocyte is an ideal model for mechanistic studies of meiosis, however, the effective methods for the analyses of spermatocytes are lacking. In this article, a practical and efficient method for the in vivo inhibition of kinesin-7 CENP-E in mouse spermatocytes is reported. A detailed procedure for testicular injection of a specific inhibitor GSK923295 through abdominal surgery in 3-week-old mice is presented. Furthermore, described here is a series of protocols for tissue collection and fixation, hematoxylin-eosin staining, immunofluorescence, flow cytometry and transmission electron microscopy. Here we present an in vivo inhibition model via abdominal surgery and testicular injection, that could be a powerful technique to study male meiosis. We also demonstrate that CENP-E inhibition results in chromosome misalignment and metaphase arrest in primary spermatocytes during meiosis I. Our in vivo inhibition method will facilitate mechanistic studies of meiosis, serve as a useful method for genetic modifications of male germ lines, and shed a light on future clinical applications.

Functional Assessment of Kinesin-7 CENP-E in Spermatocytes Using In Vivo Inhibition, Immunofluorescence and Flow Cytometry

This article reports an in vivo inhibition of CENP-E through abdominal surgery and testicular injection of GSK923295, a valuable model for male meiotic division. Using the immunofluorescence, flow cytometry and transmission electron microscopy assays, we show that CENP-E inhibition results in chromosome misalignment and genome instability in mouse spermatocytes.

In eukaryotes, meiosis is essential for genome stability and genetic diversity in sexual reproduction. Experimental analyses of spermatocytes in testes ...

CRISPR/Cas9 Gene Editing of Hematopoietic Stem and Progenitor Cells for Gene Therapy Applications

CRISPR/Cas9 is a highly versatile and efficient gene-editing tool adopted widely to correct various genetic mutations. The feasibility of gene manipulation of hematopoietic stem and progenitor cells (HSPCs) in vitro makes HSPCs an ideal target cell for gene therapy. However, HSPCs moderately lose their engraftment and multilineage repopulation potential in ex vivo culture. In the present study, ideal culture conditions are described that improves HSPC engraftment and generate an increased number of gene-modified cells in vivo. The current report displays optimized in vitro culture conditions, including the type of culture media, unique small molecule cocktail supplementation, cytokine concentration, cell culture plates, and culture density. In addition to that, an optimized HSPC gene-editing procedure, along with the validation of the gene-editing events, are provided. For in vivo validation, the gene-edited HSPCs infusion and post-engraftment analysis in mouse recipients are displayed. The results demonstrated that the culture system increased the frequency of functional HSCs in vitro, resulting in robust engraftment of gene-edited cells in vivo.

The present protocol describes an optimized hematopoietic stem and progenitor cell (HSPC) culture procedure for the robust engraftment of gene-edited cells in vivo.

CRISPR/Cas9 is a highly versatile and efficient gene-editing tool adopted widely to correct various genetic mutations. The feasibility of gene ...

Flow Cytometry Analysis of Murine Bone Marrow Hematopoietic Stem and Progenitor Cells and Stromal Niche Cells

The bone marrow (BM) is the soft tissue found within bones where hematopoiesis, the process by which new blood cells are generated, primarily occurs. As such, it contains hematopoietic stem and progenitor cells (HSPCs), as well as supporting stromal cells that contribute to the maintenance and regulation of HSPCs. Hematological and other BM disorders disrupt hematopoiesis by affecting hematopoietic cells directly and/or through the alteration of the BM niche. Here, we describe a method to study hematopoiesis in health and malignancy through the phenotypic analysis of murine BM HSPCs and stromal niche populations by flow cytometry. Our method details the required steps to enrich BM cells in endosteal and central BM fractions, as well as the appropriate gating strategies to identify the two key niche cell types involved in HSPC regulation, endothelial cells and mesenchymal stem cells. The phenotypic analysis proposed here may be combined with mouse mutants, disease models, and functional assays to characterize the HSPC compartment and its niche.

Here, we describe a simple protocol for the isolation and staining of murine bone marrow cells to phenotype hemopoietic stem and progenitor cells along with the supporting niche endothelial and mesenchymal stem cells. A method to enrich cells located in endosteal and central bone marrow areas is also included.

The bone marrow (BM) is the soft tissue found within bones where hematopoiesis, the process by which new blood cells are generated, primarily occurs. As ...