Work in Lombard laboratory is supported by the NIH (NIGMS R01GM101171, NIEHS R21ES032305), DoD (CA190267, CA170628, NF170044, and ME200030), and Glenn Foundation for Medical Research. Work in Li laboratory is supported by NIH (NHLBI 5R01HL150707).

All vertebrate animal experiments were approved by and performed in accordance with the regulations of the University of Michigan Committee on Use and Care of Animals.
1. Day before the assay (Total time: ~10 min)
<ol>
	<li>Hydration of the sensor cartridge (Step time: ~10 min)
	<ol>
		<li>Open the extracellular flux assay kit and remove the sensor cartridge and utility plate assembly. Save loading guide flats for use the next day.</li>
		<li>Manually separate the sensor cartridge (the top g...

<ol>
	<li>Rieger, M. A., Schroeder, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hematopoiesis.">Hematopoiesis.</a> Cold Spring Harbor Perspectives in Biology. 4 (12), 008250 (2012).</li><li>Papa, L., Djedaini, M., Hoffman, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+role+in+stemness+and+differentiation+of+hematopoietic+stem+cells.">Mitochondrial role in stemness and differentiation of hematopoietic stem cells.</a> Stem Cells International. 2019, 4067162 (2019).</li><li>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=Mitochondrial+regulation+of+hematopoietic+stem+cells.">Mitochondrial regulation of hematopoietic stem cells.</a> Current Opinion in Cell Biology. 49, 91-98 (2017).</li><li>Bujko, K., Kucia, M., Ratajczak, J., Ratajczak, M. Z. <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+and+progenitor+cells+(HSPCs).">Hematopoietic stem and progenitor cells (HSPCs).</a> Advances in Experimental Medicine and Biology. 1201, 49-77 (2019).</li><li>Ito, K., Suda, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Metabolic+requirements+for+the+maintenance+of+self-renewing+stem+cells.">Metabolic requirements for the maintenance of self-renewing stem cells.</a> Nature Reviews Molecular Cell Biology. 15 (4), 243-256 (2014).</li><li>Norddahl, G. 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=Accumulating+mitochondrial+DNA+mutations+drive+premature+hematopoietic+aging+phenotypes+distinct+from+physiological+stem+cell+aging.">Accumulating mitochondrial DNA mutations drive premature hematopoietic aging phenotypes distinct from physiological stem cell aging.</a> Cell Stem Cell. 8 (5), 499-510 (2011).</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>Kim, M., Cooper, D. D., Hayes, S. F., Spangrude, G. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rhodamine-123+staining+in+hematopoietic+stem+cells+of+young+mice+indicates+mitochondrial+activation+rather+than+dye+efflux.">Rhodamine-123 staining in hematopoietic stem cells of young mice indicates mitochondrial activation rather than dye efflux.</a> Blood. 91 (11), 4106-4117 (1998).</li><li>Filippi, M. D., Ghaffari, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondria+in+the+maintenance+of+hematopoietic+stem+cells:+new+perspectives+and+opportunities.">Mitochondria in the maintenance of hematopoietic stem cells: new perspectives and opportunities.</a> Blood. 133 (18), 1943-1952 (2019).</li><li>Inoue, 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=Mitochondrial+respiration+defects+modulate+differentiation+but+not+proliferation+of+hematopoietic+stem+and+progenitor+cells.">Mitochondrial respiration defects modulate differentiation but not proliferation of hematopoietic stem and progenitor cells.</a> FEBS Letters. 584 (15), 3402-3409 (2010).</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>Bhatti, J. S., Bhatti, G. K., Reddy, P. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+dysfunction+and+oxidative+stress+in+metabolic+disorders+-+A+step+towards+mitochondria+based+therapeutic+strategies.">Mitochondrial dysfunction and oxidative stress in metabolic disorders - A step towards mitochondria based therapeutic strategies.</a> Biochimica et Biophysica Acta - Molecular Basis of Disease. 1863 (5), 1066-1077 (2017).</li><li>Fontenay, M., Cathelin, S., Amiot, M., Gyan, E., Solary, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondria+in+hematopoiesis+and+hematological+diseases.">Mitochondria in hematopoiesis and hematological diseases.</a> Oncogene. 25 (34), 4757-4767 (2006).</li><li>Nadanaciva, 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=Assessment+of+drug-induced+mitochondrial+dysfunction+via+altered+cellular+respiration+and+acidification+measured+in+a+96-well+platform.">Assessment of drug-induced mitochondrial dysfunction via altered cellular respiration and acidification measured in a 96-well platform.</a> Journal of Bioenergetics and Biomembranes. 44 (4), 421-437 (2012).</li><li>Nicholls, D. G., 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=Bioenergetic+profile+experiment+using+C2C12+myoblast+cells.">Bioenergetic profile experiment using C2C12 myoblast cells.</a> Journal of Visualized Experiments: JoVE. (46), e2511 (2010).</li><li>Mookerjee, S. A., Goncalves, R. L. S., Gerencser, A. A., Nicholls, D. G., Brand, M. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+contributions+of+respiration+and+glycolysis+to+extracellular+acid+production.">The contributions of respiration and glycolysis to extracellular acid production.</a> Biochimica et Biophysica Acta. 1847 (2), 171-181 (2015).</li><li>Nicholls, D. G., Ferguson, S. J., Nicholls, D. G., Ferguson, 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=.">.</a> Bioenergetics, Fourth Edition. , 255-302 (2013).</li><li>Aft, R. L., Zhang, F. W., Gius, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+2-deoxy-D-glucose+as+a+chemotherapeutic+agent:+mechanism+of+cell+death.">Evaluation of 2-deoxy-D-glucose as a chemotherapeutic agent: mechanism of cell death.</a> British Journal of Cancer. 87 (7), 805-812 (2002).</li><li>Traba, J., Miozzo, P., Akkaya, B., Pierce, S. K., Akkaya, M. <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+protocol+to+analyze+glycolysis+and+mitochondrial+respiration+in+lymphocytes.">An Optimized protocol to analyze glycolysis and mitochondrial respiration in lymphocytes.</a> Journal of Visualized Experiments: JoVE. (117), e54918 (2016).</li><li>Horan, M. P., Pichaud, N., Ballard, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Review:+quantifying+mitochondrial+dysfunction+in+complex+diseases+of+aging.">Review: quantifying mitochondrial dysfunction in complex diseases of aging.</a> The Journals of Gerontology, Series A: Biological Sciences and Medical Sciences. 67 (10), 1022-1035 (2012).</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></ol>

This method paper describes an optimized protocol for the assessment of cellular bioenergetics (glycolysis and OxPHOS) in mouse HSPCs using the Seahorse extracellular flux analyzer. This device is a powerful tool that simultaneously measures the ECAR and OCR of live cells, which are metrics of glycolysis and mitochondrial respiration, respectively. Thus, it can be used to assess the cellular bioenergetics in real time. Further, the 96-well microplate-based platform offers high-throughput quantification with high sensitiv...

Hematopoiesis is the process by which various types of mature blood cells with highly specialized functions are formed from HSCs1. HSCs are capable of self-renewal and differentiation into various multipotent and lineage-specific progenitor populations. These progenitors ultimately produce cells of lymphoid, myeloid, erythroid, and megakaryocyte lineages. To maintain their self-renewal capacity, HSCs remain largely quiescent and, like other tissue stem cells, are believed to rely on glycolysis rather than mitochondrial OxPHOS for ATP production2,3. Entry into the cell cycle leads to enhanced respiration and OxPHOS, resulting in elevated levels of reactive oxygen species (ROS), which are detrimental to HSC maintenance and function3. Repeated cell division thus may lead to reduced self-renewal capacity of HSCs and ultimately to their exhaustion.
In adult hematopoiesis, HSCs primarily undergo asymmetric cell division, during which one of the daughter cells retains HSC potential and continues to rely on glycolytic metabolism. The other daughter cell becomes a primitive progenitor cell that loses self-renewal capacity but proliferates and eventually gives rise to differentiated functional hematopoietic cells4. When HSCs differentiate to produce downstream progenitors, a switch from glycolysis to mitochondrial metabolism is thought to occur to supply the energy and building blocks needed to support this rapid transition5, as suggested by the observations that HSCs possess inactive mitochondrial mass6,7,8,9. In contrast, mitochondrial activity (indicated by linked ROS levels) is much higher in lineage-committed progenitors than in HSCs9,10,11. Metabolic changes that occur during the earliest step of hematopoiesis thus suggest a direct and crucial role of mitochondria in regulating HSC fate.
Dysfunctional mitochondria present under various stress conditions, such as aging, cancer, diabetes, and obesity12, can interfere with HSC self-renewal capacity, inducing an imbalance in HSC/progenitor differentiation by producing excessive amounts of ROS, impairing ATP production, and/or by altering other metabolic processes9,12,13. Perturbations in metabolic homeostasis in HSC/progenitor differentiation could significantly impact hematopoiesis, potentially contributing to the development of hematologic abnormalities13. Given the critical influences of glycolysis and mitochondrial OxPHOS on HSC stemness and differentiation, it is of interest to investigate both metabolic parameters under normal and stress conditions. Valuable insights into the glycolytic and mitochondrial function of HSCs and progenitor cells can be gained by assessing their ECAR and OCR, which are indicators of cellular glycolysis and mitochondrial respiration, respectively.
The Seahorse extracellular flux analyzer is a powerful apparatus equipped with two probes per well to simultaneously measure ECAR and OCR in live cells and thus can be used to assess cellular bioenergetics in real time, in response to various substrates or inhibitors. The assay cartridge used with the analyzer contains injection ports to hold up to four drugs for automated injection during the assay. A scheme of a typical glycolysis stress test is shown in Figure 1A. The assay starts with the measurement of ECAR of cells, incubated in glycolysis stress test medium containing glutamine but not glucose or pyruvate. This represents acidification occurring due to non-glycolytic activities of the cells and is reported as non-glycolytic acidification. This is followed by the injection of glucose at a saturating concentration. Via glycolysis, glucose in the cell is converted into pyruvate, which is further metabolized in the cytoplasm to produce lactate, or in mitochondria to produce CO2 and water.
Conversion of glucose to lactate causes net production and subsequent release of protons into the extracellular medium, resulting in a rapid increase in the ECAR14,15,16. This glucose-stimulated change in ECAR is reported as glycolysis under basal conditions. The second injection consists of oligomycin (an inhibitor of ATP synthase, a.k.a. complex V17), which inhibits mitochondrial ATP production. During oligomycin-mediated OxPHOS inhibition, cells maximally upregulate glycolysis to meet their energetic demands. This causes a further increase in ECAR, revealing the maximum glycolytic capacity of the cells. The difference between the maximum glycolytic capacity and basal glycolysis is referred to as glycolytic reserve. Finally, 2-DG is injected, which causes a significant drop in ECAR, usually close to non-glycolytic acidification levels. 2-DG is a glucose analog that competitively binds to hexokinase, resulting in inhibition of glycolysis18. Thus, the 2-DG-induced decrease in ECAR further confirms that glycolysis is indeed the source of ECAR observed after glucose and oligomycin injections.
Figure 1B displays the schematic for a typical mitochondrial stress test. The assay starts with baseline OCR measurement of the cells, incubated in mitochondrial stress test medium containing glucose, glutamine, and pyruvate. Following basal OCR measurements, oligomycin is injected in this assay, which inhibits complex V, thereby reducing electron flow through the electron transport chain (ETC)17. Consequently, OCR is reduced in response to oligomycin injection, and this decrease in OCR is linked to mitochondrial ATP production. The second injection consists of carbonyl cyanide-4 (trifluoromethoxy) phenylhydrazone (FCCP), a protonophore and an uncoupler of mitochondrial OxPHOS17. FCCP collapses the mitochondrial proton gradient by allowing the flow of protons across the mitochondrial inner membrane. Because of the FCCP injection, electron flow through the ETC is derepressed, and complex IV consumes oxygen at the maximal level. The difference between maximal OCR and basal OCR is referred to as the spare respiratory capacity, which is a measure of the cell&#39;s ability to respond to increased energy demand under stress conditions. Finally, a mixture of two ETC inhibitors (rotenone, a complex I inhibitor, and antimycin A, a complex III inhibitor17) is injected, which completely shuts down electron flow, and OCR decreases to a low level. OCR measured after rotenone and antimycin A injection corresponds to non-mitochondrial OCR driven by other processes inside the cells. Non-mitochondrial OCR enables the calculation of basal respiration, proton leak, and maximal respiration.
Basal respiration represents the difference between baseline OCR and non-mitochondrial OCR. Proton leak refers to the difference between OCR after oligomycin injection and non-mitochondrial OCR. Maximal respiration represents the difference between OCR after FCCP injection and non-mitochondrial OCR. Coupling efficiency is calculated as the percentage of ATP production rate to basal respiration rate. This method paper provides a detailed protocol to measure ECAR and OCR in lineage-negative HSPCs using the Seahorse XFe96 extracellular flux analyzer. This protocol describes approaches to isolate mouse lineage-negative HSPCs, explains the optimization of cell-seeding density and concentrations of various drugs used in extracellular flux assays, and describes drug treatment strategies.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.2 &#956;m filter</td>
			<td>Corning</td>
			<td>430626</td>
			<td>Used to filter-sterilize the assay media</td>
		</tr>
		<tr>
			<td>100 mM sodium pyruvate</td>
			<td>Life Technologies</td>
			<td>11360-070</td>
			<td>Component of mitochondrial stress test assay medium</td>
		</tr>
		<tr>
			<td>15 mL conical Falcon tubes</td>
			<td>Corning</td>
			<td>352096</td>
			<td>Used during HSPCs harvest and to prepare assay drug solutions</td>
		</tr>
		<tr>
			<td>200 mM L-glutamine</td>
			<td>Life Technologies</td>
			<td>25030-081</td>
			<td>Component of glycolysis stress test and mitochondrial stress test assay media</td>
		</tr>
		<tr>
			<td>2-Deoxy-D-glucose (2-DG)</td>
			<td>Sigma-Aldrich</td>
			<td>D8375</td>
			<td>3rd drug injection during glycolysis stress test</td>
		</tr>
		<tr>
			<td>5x Enrichment buffer (MojoSort)</td>
			<td>Biolegend</td>
			<td>480017</td>
			<td>Used for washings during HSPCs harvest</td>
		</tr>
		<tr>
			<td>Ammonium chloride (NH4Cl)</td>
			<td>Fisher Scientific</td>
			<td>A661-3</td>
			<td>Component of ACK lysis buffer</td>
		</tr>
		<tr>
			<td>Antimycin A</td>
			<td>Sigma-Aldrich</td>
			<td>A8674</td>
			<td>3rd drug injection during mitochondrial stress test</td>
		</tr>
		<tr>
			<td>Bio-Rad DC protein assay kit</td>
			<td>Bio-Rad</td>
			<td>500-0112</td>
			<td>Used as per manufacturer&#39;s instructions</td>
		</tr>
		<tr>
			<td>Carbonyl cyanide-4 (trifluoromethoxy) phenylhydrazone (FCCP)</td>
			<td>Sigma-Aldrich</td>
			<td>C2920</td>
			<td>2nd drug injection during mitochondrial stress test</td>
		</tr>
		<tr>
			<td>Cell-Tak</td>
			<td>Corning</td>
			<td>354240</td>
			<td>Cell adhesive. Used for coating cell microplates</td>
		</tr>
		<tr>
			<td>Countes 3 Automated Cell Counter</td>
			<td>ThermoFisher Scientific</td>
			<td></td>
			<td>For cell counting</td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Fisher Scientific</td>
			<td>O2793-500</td>
			<td>Component of ACK lysis buffer and RIPA lysis buffer</td>
		</tr>
		<tr>
			<td>Falcon 70 &#956;m filter</td>
			<td>Fisher Scientific</td>
			<td>08-771-2</td>
			<td>Used as cells strainer during HSPCs harvest</td>
		</tr>
		<tr>
			<td>Gibco Fetal bovine serum (FBS)</td>
			<td>Fisher Scientific</td>
			<td>26400044</td>
			<td>Used to prepare assay buffer during HSPCs harvest</td>
		</tr>
		<tr>
			<td>Gibco HBSS</td>
			<td>Fisher Scientific</td>
			<td>14175095</td>
			<td>Used to prepare assay buffer during HSPCs harvest</td>
		</tr>
		<tr>
			<td>Glucose</td>
			<td>Sigma-Aldrich</td>
			<td>G7528</td>
			<td>Component of mitochondrial stress test assay medium and first injection of glycolysis stress test</td>
		</tr>
		<tr>
			<td>Oligomycin</td>
			<td>Sigma-Aldrich</td>
			<td>O4876</td>
			<td>2nd drug injection during glycolysis stress test and 1st drug injection during mitochondrial stress test</td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Life Technologies</td>
			<td>10010-049</td>
			<td>Used to wash cells after assay for protein quantification</td>
		</tr>
		<tr>
			<td>Potassium bicarbonate (KHCO3)</td>
			<td>Fisher Scientific</td>
			<td>P235-500</td>
			<td>Component of ACK lysis buffer</td>
		</tr>
		<tr>
			<td>Protease Inhibitor Cocktail (PIC)</td>
			<td>Roche</td>
			<td>11836170001</td>
			<td>Supplied as tablets. One tablet was dissolved in 10 mL of RIPA buffer to make 1x PIC.</td>
		</tr>
		<tr>
			<td>Rat biotin antimouse-B220, Clone ID: RA3-6B2</td>
			<td>Biolegend</td>
			<td>103203</td>
			<td>Used for lineage depletion during HSPCs harvest</td>
		</tr>
		<tr>
			<td>Rat biotin antimouse-CD2, Clone ID: RM2-5</td>
			<td>Biolegend</td>
			<td>100103</td>
			<td>Used for lineage depletion during HSPCs harvest</td>
		</tr>
		<tr>
			<td>Rat biotin antimouse-CD3, Clone ID: 17A2</td>
			<td>Biolegend</td>
			<td>100243</td>
			<td>Used for lineage depletion during HSPCs harvest</td>
		</tr>
		<tr>
			<td>Rat biotin antimouse-CD5, Clone ID: 53-7.3</td>
			<td>Biolegend</td>
			<td>100603</td>
			<td>Used for lineage depletion during HSPCs harvest</td>
		</tr>
		<tr>
			<td>Rat biotin antimouse-CD8, Clone ID: 53-6.7</td>
			<td>Biolegend</td>
			<td>100703</td>
			<td>Used for lineage depletion during HSPCs harvest</td>
		</tr>
		<tr>
			<td>Rat biotin antimouse-Gr-1, Clone ID: RB6-8C5</td>
			<td>Biolegend</td>
			<td>108403</td>
			<td>Used for lineage depletion during HSPCs harvest</td>
		</tr>
		<tr>
			<td>Rat biotin antimouse-Ter-119, Clone ID: TER-119</td>
			<td>Biolegend</td>
			<td>116203</td>
			<td>Used for lineage depletion during HSPCs harvest</td>
		</tr>
		<tr>
			<td>Rotenone</td>
			<td>Sigma-Aldrich</td>
			<td>R8875</td>
			<td>3rd drug injection during mitochondrial stress test</td>
		</tr>
		<tr>
			<td>Seahorse XFe96 extracellular flux analyzer</td>
			<td>Seahorse Biosciences now Agilent</td>
			<td></td>
			<td>For ECAR and OCR measurments in real time.</td>
		</tr>
		<tr>
			<td>Sodium bicarbonate</td>
			<td>Sigma-Aldrich</td>
			<td>S5761</td>
			<td>Used to make Cell-adhesive solution for microplate coating</td>
		</tr>
		<tr>
			<td>Sodium chloride (NaCl)</td>
			<td>Fisher</td>
			<td>BP358</td>
			<td>Component of RIPA lysis buffer</td>
		</tr>
		<tr>
			<td>Sodium deoxycholate</td>
			<td>Sigma-Aldrich</td>
			<td>D6750</td>
			<td>Component of RIPA lysis buffer</td>
		</tr>
		<tr>
			<td>Sodium Fluoride (NaF)</td>
			<td>Sigma-Aldrich</td>
			<td>S7920</td>
			<td>Component of RIPA lysis buffer</td>
		</tr>
		<tr>
			<td>Sodium hydroxide (NaOH)</td>
			<td>Sigma-Aldrich</td>
			<td>S8045</td>
			<td>Prepared 1 N solution. Used for pH normalization</td>
		</tr>
		<tr>
			<td>Streptavidin Nanobeads (MojoSort)</td>
			<td>Biolegend</td>
			<td>480015</td>
			<td>Used for lineage depletion during HSPCs harvest</td>
		</tr>
		<tr>
			<td>Tris-HCl</td>
			<td>Fisher</td>
			<td>BP153</td>
			<td>Component of RIPA lysis buffer</td>
		</tr>
		<tr>
			<td>XF base medium</td>
			<td>Agilent</td>
			<td>102353-100</td>
			<td>base medium used to prepare glycolysis stress test and mitochondrial stress test assay media</td>
		</tr>
		<tr>
			<td>XF prep station</td>
			<td>Seahorse Biosciences</td>
			<td></td>
			<td>Used for non-CO2 37 &#176;C incubations</td>
		</tr>
		<tr>
			<td>XFe96 extracellular FluxPak</td>
			<td>Agilent</td>
			<td>102416-100 or 102601-100</td>
			<td>Includes assay cartridges with utility plates, loading guide flats for loading 
			drugs onto the assay cartridge, XF calibrant solution, and XF cell culture microplate</td>
		</tr>
	</tbody>
</table>

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.

Using this protocol, the cell number and the concentrations of various OxPHOS-targeting drugs (used in the extracellular flux assays) were optimized to measure ECAR and OCR of HSPCs isolated from 24-week-old female C57BL/6 mice. First, the glycolysis stress test was performed to optimize cell number and oligomycin concentration. A varying number of HSPCs per well ranging from 5 &#215; 104 to 2.5 &#215; 105 were used in this assay. As shown in Figure 2A and <strong class...

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

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 ...

During hematopoiesis, hematopoietic stem cells undergo a metabolic switch from glycolysis to oxidative phosphorylation. This protocol can be used to assess glycolytic and mitochondrial functions of mouse hematopoietic stem and progenitor cells. This method can be used to assess cellular bioenergetics in real time.The 96-well microplate-based platform offers high throughput quantification with high sensitivity, allowing simultaneous analysis of multiple samples using a single plate. This technique can be used to probe the effects of chemicals or genetic manipulations on HSC metabolism under varied conditions. It can help elucidate metabolic pathways that sustain HSC pluripotency.Although the current study is mainly focused on mouse hematopoietic stems and progenitor cells, the protocol and this approach could easily be adapted to optimize analysis conditions for any type of suspension cells. One day before the assay, open the extracellular flux assay kit to remove the sensor cartridge and utility plate assembly. Save the loading guide flats for use the next day.Now manually separate the sensor cartridge from the utility plate and place it upside down next to the utility plate. Using a multichannel pipette, fill each well of the utility plate with 200 microliters of calibrant included with the flux assay kit, then place the sensor cartridge back onto the utility plate, making sure to completely submerge the sensors in the calibrant. Then incubate the utility plate with calibrant and assembled sensor cartridge in a non-carbon dioxide incubator at 37 degrees Celsius overnight following the humidifying conditions mentioned in the manuscript.On the day of the assay, prepare 2.5 milliliters of the cell adhesive solution per 96-well cell culture microplate as described in the text manuscript. Open the 96-well cell culture microplate included with the flux assay kit and dispense 25 microliters of the prepared cell adhesive solution at the bottom of each well. Cover the microplate with the lid and incubate for 30 minutes at room temperature inside the hood.After incubation, remove and discard the excess cell adhesive solution using a multichannel pipette or aspirator and wash each well twice with 200 microliters of sterile ultrapure water. Air dry the plate without the lid inside the hood for 30 to 45 minutes. Centrifuge the prepared mouse lineage negative HSPCs at 200 times G for five minutes at room temperature.After discarding the supernatant, resuspend the cell pellet in the appropriate assay medium, and again centrifuge the cell suspension. Repeat this procedure one more time and resuspend the cells in the appropriate warmed assay medium to the concentration of 250, 000 cells per 50 microliters or five million cells per milliliters. Use a multichannel pipette to add 50 microliters of the cell suspension along the side of each well of the cell adhesive coated 96-well cell culture microplate, then add 50 microliters of the assay medium into the corner background measurement wells.Create a centrifuge balance plate by adding 50 microliters of water per well of a non-coated 96-well cell culture microplate. Centrifuge the cells at 200 times G for one minute at room temperature. Incubate the plate in a non-carbon dioxide incubator at 37 degrees Celsius for 25 to 30 minutes for cell attachment.After 30 minutes, visually confirm under a microscope that the cells are stably adhered to the microplate surface. Begin by preparing all the required solutions in the pre-warmed glycolysis stress test assay medium as mentioned in the text manuscript and remove the hydrated sensor cartridge from the incubator. Lift the sensor cartridge out of the calibrant and replace it on the same utility plate with the calibrant to remove the air bubbles.Place the 80 loading guide flat on the top of the sensor cartridge orienting it so that the letter A is located on the upper left-hand corner. Using a multichannel pipette, dispense 20 microliters of 100 millimolar glucose solution in port A.Replace the 80 loading guide flat with the BC loading guide flat, orienting the letter B on the upper left-hand corner. Dispense 22 microliters of 20 micromolar oligomycin solution in port B.Reorient the BC loading guide flat to locate the letter C on the upper left-hand corner for loading port C and dispense 25 microliters of 500 millimolar 2-deoxy-d-glucose solution in port C.Then remove and discard the loading guide flats.Now create or load the template for the glycolysis stress test on the controller. Enter the details regarding injection strategies, treatment conditions, and cell types, and press Generate Groups. Go to the plate map and assign wells to each group to be analyzed.In the protocol, ensure that calibration and equilibration are checked in the initialization step. For the baseline measurement and measurements after each injection, set the number of measurement cycles to three and mix, wait, measure times to three minutes, zero minutes, three minutes. Click Start Run on the software.Remove the lid from the compounds loaded and hydrated sensor cartridge and place it on the work tray of the extracellular flux analyzer. Begin the calibration run. Take out the microplate containing the seeded cells from the incubator.Without disturbing the cells, slowly add 130 microliters of the pre-warmed glycolysis stress test assay medium per well to make up the medium volume in each well to 180 microliters and return the plate to the incubator for an additional 15 to 20 minutes. Click Open Tray on the software to open the thermal tray of Seahorse. After the calibration is over, replace the utility plate with this assay microplate containing the cells and press the Load Cell Plate to start the measurements.After the measurements are over, remove the assay medium from the plate without disturbing the cells and wash them gently with 250 microliters of phosphate buffered saline without dislodging the cells. Now add 10 microliters of radioimmunoprecipitation lysis buffer supplemented with 1X protease inhibitor cocktail to each well and agitate the plate on a shaker for 10 minutes. Freeze the whole plate at minus 80 degrees Celsius.Thaw the plate and perform a protein measurement assay for data normalization following the manufacturer's instructions. Retrieve and analyze the data by opening the data file using Wave desktop software. Click on Normalize, paste the normalization values for each well and then click on Apply to normalize the data.Click on Export and select glycolysis stress test report generator to export the analyzed data to a report generator. The non-glycolytic acidification rate rises with increased cell number from 50, 000 to 250, 000, but increases only minimally between 200, 000 to 250, 000. Injection of 10 millimolar glucose stimulates glycolysis at all cell numbers with a maximum increase in ECAR observed at 250, 000 cells per well.However, injection of two micromolar of oligomycin does not further increase ECAR. The OCR data obtained in the same set of glycolysis stress tests show a significant drop following oligomycin injection due to complex 5 inhibition. Glycolysis stress test parameters were calculated and 250, 000 cells per well in two micromolar of oligomycin were selected for further studies.The mitochondrial stress test showed that two micromolar oligomycin injection causes a significant reduction in OCR via the inhibition of complex 5. FCCP stimulates OCR in HSPCs in a dose-dependent manner with a maximal increase observed at two micromolar. A mixture of 0.5 micromolar rotenone and 0.5 micromolar antimycin A injection decreases OCR to its minimal level corresponding to non-mitochondrial oxygen consumption.Mitochondrial stress test parameters were calculated and two micromolar of FCCP was selected for further studies. Given the high throughput nature of this technique, the protocol described here could easily be adapted to screen a large number of bioenergetic modulators in hematopoietic stem cells, hematopoietic progenitors, and malignant hematopoietic cells. Seahorse analysis is widely used in the literature to measure metabolism in a wide variety of contexts in the presence of various substrates and inhibitors.

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2.4K Views.  University of Michigan, Ann Arbor. During hematopoiesis, hematopoietic stem cells undergo a metabolic switch from glycolysis to oxidative phosphorylation. This protocol can be used to assess glycolytic and mitochondrial functions of mouse hematopoietic stem and progenitor cells. This method can be used to assess cellular bioenergetics in real time.The 96-well microplate-based platform offers high throughput quantification with high sensitivity, allowing simultaneous analysis of multiple samples using a single plate. Thi...