We thank the UNIL Flow Cytometry Core Facility for their support especially Dr. Romain Bedel. This work was supported by the Kristian Gerhard Jebsen foundation grant to N.V and O.N.

All experiments described in the manuscript follow the guidelines of our institution and were carried out in accordance with Swiss law for animal experimentation (Authorization: VD3194) and for research involving human samples (Protocol: 235/14; CER-VD 2017-00490)
1. Hematopoietic Stem Cell Extraction
<ol>
	<li>Purchase wild type C57BL6/J mice and keep them in the animal house for at least a week to reduce transport-associated stress.</li>
	<li>On the day of the experiment, euthanize the mouse using CO2 asphyxiation.</li>
	<li>Spray the mouse with 70% ethanol to sterilize the fur and cut open the mouse at the belly using standard surgical tools, such as dissection scissors and forceps, to cut the femur and tibia bones from the hind legs.</li>
	<li>Remove the muscles attached to the femur, tibia, and the pelvis using a soft paper towel and place the cleaned bones in a 50 mL tube containing PBS with 1 mM EDTA (buffer) on ice.</li>
	<li>Spray a mortar and pestle with 70% ethanol and place it in a cell culture hood. Sterilize it with UV for 30 min. Post sterilization rinse the mortar and pestle with buffer to remove traces of ethanol.</li>
	<li>Put the clean bones with some buffer (~10 mL) in the mortar and gently crush them to get the bone marrow out in suspension. Now, collect the cell suspension and pass it through a 70 &#181;m cell strainer into a 50 mL tube to get a single cell suspension.</li>
	<li>Repeat step 1.6 until all the bone marrow has been extracted and the bone debris has turned white.</li>
	<li>Place the 50 mL tube(s) containing the bone marrow single cell suspension on a centrifuge. Run the centrifuge at 300 x g for 10 min at 4 &#176;C to pellet the cells.</li>
	<li>Meanwhile, prepare 10 mL of 1x RBC lysis buffer in autoclaved distilled water. Filter the solution through a 0.22 &#181;m filter.</li>
	<li>Collect the sample tube from the centrifuge and decant the supernatant. Pipette the 1x RBC lysis buffer (Table of Materials) on the cell pellet. Dislodge the pellet and prepare a homogenous solution by pipetting up and down a few times. Allow the tube to be at room temperature for 1&#8211;2 min for the RBC lysis to occur. Stop the lysis process by filling up the tube with the buffer.</li>
	<li>Place the tube on a centrifuge and spin at 300 x g for 5 min at 4 &#176;C. Collect the tube from the centrifuge and decant the supernatant. Resuspend the pellet by adding 10 mL of buffer and filter the solution into a new 50 mL tube via a 70 &#181;m cell strainer to remove the debris due to RBC lysis.</li>
	<li>Centrifuge the tube at 300 x g for 5 min at 4 &#176;C. Collect the tube from the centrifuge and decant the supernatant. Resuspend the pellet in 500 &#181;L of buffer.</li>
	<li>Remove a 100 &#181;L aliquot and keep in a separate 1.5 mL tube. Add 50 &#181;L of biotin lineage depletion antibody cocktail from the progenitor enrichment kit (Table of Materials) to the remaining 450 &#181;L of cell suspension. Incubate at 4 &#176;C on a shaker for 15 min.</li>
	<li>Add 15 mL of buffer and centrifuge the tube at 300 x g for 5 min at 4 &#176;C. Collect the tube from the centrifuge and decant the supernatant. Resuspend the pellet in 460 &#181;L of buffer. Remove a 10 &#181;L aliquot and keep in a separate 1.5 mL tube.</li>
	<li>Add 50 &#181;L of streptavidin magnetic beads from the progenitor enrichment kit (Table of Materials), to the remaining 450 &#181;L cell suspension. Incubate at 4 &#176;C on a shaker for 15 min.</li>
	<li>Add 15 mL of buffer and centrifuge the tube at 300 x g for 5 min at 4 &#176;C. Collect the tube from the centrifuge and decant the supernatant. Resuspend the pellet in 5 mL of buffer and transfer the solution to a 15 mL tube.</li>
	<li>Take the tube to an automated cell separator (Table of Materials). Run a wash program to rinse and prime the tubing of the cell separator. Place the sample and two collection tubes on the tube holder. Perform separation using the &#34;Deplete&#34; program. Collect the positive and the negative fractions from the automated cell separator once the run has ended. 
	NOTE: In the absence of an automatic cell separator the users can use manual magnetic columns and corresponding magnets, per the user manual. The users should keep in mind that the process of manual separation is slower than the automated one. Also, the manual columns are more prone to clogging. Therefore, users are advised to dilute the sample and load on the column slowly.</li>
	<li>Discard the positive fraction. Fill the negative fraction tube with buffer. Centrifuge the tube at 300 x g for 5 min at 4 &#176;C.</li>
	<li>Meanwhile, prepare the antibody mix in 1 mL of final volume solution and the single-color controls in 200 &#181;L of final volume solution as described in Table of Materials and Table 1. 
	NOTE: If the TMRM and the green fluorescent mitochondrial stain are to be combined with stem cell marker staining, then replace CD150-PE with CD150-PEcy5 and Streptavidin-Tx red with Streptavidin-Pac Orange.</li>
	<li>Collect the sample tube from the centrifuge and decant the supernatant. Resuspend the pellet in 1 mL of antibody mix. Add 10 &#181;L of cells (from step 1.13) in each of the single-color control tubes (except lineage). Add 10 &#181;L of cells (from step 1.14) in the lineage single color tube.</li>
	<li>Incubate the sample and single-color control tubes at 4 &#176;C on a shaker for 45 min. Cover the ice bucket with a lid or aluminum foil.</li>
	<li>Fill all tubes with buffer and centrifuge at 300 x g for 5 min at 4 &#176;C. Discard the supernatant and resuspend the sample in 1 mL of buffer and single-color controls in 200 &#181;L of buffer.</li>
	<li>Transfer the sample and the single-color controls to 5 mL filter top FACS tubes.</li>
	<li>Take the tubes to the sorting machine and sort the HSC population (gating strategy in Figure 1A) in 1.5 mL tubes containing 400 &#181;L of stem cell expansion medium.</li>
</ol>
2. Ex Vivo Culture of Hematopoietic Stem Cells
<ol>
	<li>Collect tubes containing sorted cells (see section 1 for cell extraction). Centrifuge the tubes at 300 x g for 5 min at 4 &#176;C. Gently remove most of the supernatant without dislodging the pellet and leave 50&#8211;80 &#181;L on top of the cell pellet. This minimizes cell loss.</li>
	<li>Resuspend the cell pellet in stem cell expansion medium to a final volume dependent on the number of conditions to be tested (count for 100 &#181;L per well/condition of culture).</li>
	<li>Prepare a 2x culture medium containing stem cell expansion medium, stem cell factor (200 ng/mL), FLT3 ligand (4 ng/mL) and pen-strep antibiotics (1%) (2x basal medium; Table of Materials).</li>
	<li>Take a sterile tissue culture treated 96 U-bottom well plate (Table of Materials) and identify the wells where the cells will be cultured (plate design in Figure 1B). 
	NOTE: Users are advised to avoid marginal wells, as they are more susceptible to evaporation.</li>
	<li>Put 100 &#181;L of 2x basal medium previously prepared in step 2.3 in these wells. In the NR marked well add 2 &#181;L of a 100x NR solution (Table of Materials). Replenish NR every 24 h. 
	NOTE: Replenishment is specific to NR. Other metabolic modulators may or may not need replenishment.</li>
	<li>Seed 100 &#181;L of cells prepared in step 2.2 on top of the wells containing 2x basal medium. In this experiment the number of HSCs seeded per well were between 800&#8211;1,000 cells.</li>
	<li>Prepare five extra wells containing 2x basal medium. In each of these add 100,000 whole bone marrow cells (from step 1.13) resuspended in 100 &#181;L of stem cell expansion medium to be used as staining controls for post culture flow cytometry analysis. 
	NOTE: If users want to combine stem cell markers and mitochondrial markers for post culture analysis it is recommended to additionally sort the progenitor population (either Ckit+ cells or LKSCD150- cells). Seed these sorted progenitors in the staining control wells for post culture flow cytometry analysis. Prepare one well per single stain color.</li>
	<li>Put 200 &#181;L of autoclaved water in all surrounding wells to reduce evaporation from wells containing cells. Leave the plate undisturbed in an incubator at 37 &#176;C and 5% CO2 for the duration of the culture period (72 h). Remove the plate to replenish NR every 24 h and place it back in the incubator.</li>
</ol>
3. Measurement of Mitochondrial Mass and Membrane Potential
<ol>
	<li>At the end of the culture period prepare a 100x solution of TMRM (20 &#181;M) and Mitotracker green (10 &#181;M) (green fluorescent stain) in stem cell expansion medium (Table of Materials).</li>
	<li>Add 2 &#181;L of 100x TMRM solution and 2 &#181;L of 100x green fluorescent stain solution in each of the test wells. Add 2 &#181;L of 100x TMRM in the TMRM control well. Add 2 &#181;L of 100x green fluorescent stain in the Mitotracker control well. Place the plate back in an incubator at 37 &#176;C and 5% CO2 for 45 min. Cover the top of the plate with aluminum foil. 
	NOTE: An additional control with Verapamil (ABC pump inhibitor) can be prepared if ABC pump mediated dye efflux needs to be tested. For this, add 50 &#181;M Verapamil in one of the test wells 1 h before staining for TMRM and green fluorescent stain.</li>
	<li>Remove the plate from the incubator and centrifuge it at 300 x g for 5 min. Invert the plate to remove the supernatant. Add 200 &#181;L of standard FACS buffer (PBS-1 mM EDTA-P/S-2% FBS), centrifuge the plate at 300 x g for 5 min. Remove the supernatant. Repeat this washing step 3x. The users must ensure that the plate is always covered with foil, to provide minimal exposure to direct light. 
	NOTE: If users need to combine the mitochondrial staining with stem cell staining, the sample will need to be incubated with an antibody mix of all stem cell markers and the single-color controls will need to be stained with individual antibodies separately at 4 &#176;C for 30&#8211;45 min. 
	NOTE: At all steps users must keep the plate covered with aluminum foil. Users must note that this additional staining step and subsequent washing steps can result in additional cell loss.</li>
	<li>Resuspend the cells in 200 &#181;L of FACS buffer and transfer to FACS tubes.</li>
	<li>Run the samples on the flow cytometer (see Figure 1). Single color tubes containing WBM include: (1) Unstained; (2) DAPI; (3) TMRM (PE); (4) green fluorescent stain (FITC); (5) Full stain (PE and FITC).</li>
	<li>First acquire the single-color controls to set up the machine. Use the running software on the machine to calculate the compensation. Once compensation has been applied, acquire the HSC sample and record as many events as possible. 
	NOTE: If the stem cell and mitochondrial markers are combined, the users need to be particularly careful with compensation between TMRM (PE), CD150 (PE-Cy5), and Sca-1 (APC). Also, the samples should be run immediately post staining.</li>
	<li>Export the FACS files from the cytometer and analyze the data on an analysis software (Table of Materials).
	<ol>
		<li>For the analysis, open the file on the analysis software. Using FSC-A and SSC-A gating identify the cell population. Identify singlets in the next gates before plotting the DAPI negative fraction (live cells). In the live cell gate make a contour plot in the TMRM and green fluorescent stain channel to measure &#916;&#936;m and mass, respectively (Figure 2A). Export the mean fluorescence intensity (MFI) of these two channels in the live cell gate.</li>
		<li>The TMRM low gate is set based on the shoulder population in the TMRM channel. The TMRM single-color control can be used to identify this shoulder population to set the gate. Export the proportion of live of cells in the TMRM low gate in your control and test samples for plotting.</li>
	</ol>
	</li>
</ol>

<ol>
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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=Metabolic+regulation+by+the+mitochondrial+phosphatase+PTPMT1+is+required+for+hematopoietic+stem+cell+differentiation.">Metabolic regulation by the mitochondrial phosphatase PTPMT1 is required for hematopoietic stem cell differentiation.</a> Cell Stem Cell. 12 (1), 62-74 (2013).</li><li>Chen, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=TSC-mTOR+maintains+quiescence+and+function+of+hematopoietic+stem+cells+by+repressing+mitochondrial+biogenesis+and+reactive+oxygen+species.">TSC-mTOR maintains quiescence and function of hematopoietic stem cells by repressing mitochondrial biogenesis and reactive oxygen species.</a> Journal of Experimental Medicine. 205 (10), 2397-2408 (2008).</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=Regulation+of+oxidative+stress+by+ATM+is+required+for+self-renewal+of+haematopoietic+stem+cells.">Regulation of oxidative stress by ATM is required for self-renewal of haematopoietic stem cells.</a> Nature. 431 (7011), 997-1002 (2004).</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=Reactive+oxygen+species+act+through+p38+MAPK+to+limit+the+lifespan+of+hematopoietic+stem+cells.">Reactive oxygen species act through p38 MAPK to limit the lifespan of hematopoietic stem cells.</a> Nature Medicine. 12 (4), 446-451 (2006).</li><li>Tothova, Z., 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=FoxOs+are+critical+mediators+of+hematopoietic+stem+cell+resistance+to+physiologic+oxidative+stress.">FoxOs are critical mediators of hematopoietic stem cell resistance to physiologic oxidative stress.</a> Cell. 128 (2), 325-339 (2007).</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, (2016).</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 (2019).</li><li>Gratwohl, 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=Risk+score+for+outcome+after+allogeneic+hematopoietic+stem+cell+transplantation:+a+retrospective+analysis.">Risk score for outcome after allogeneic hematopoietic stem cell transplantation: a retrospective analysis.</a> Cancer. 115 (20), 4715-4726 (2009).</li><li>Gooley, T. 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J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=T+cell+exhaustion.">T cell exhaustion.</a> Nature Immunology. 12 (6), 492-499 (2011).</li><li>Ho, P. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phosphoenolpyruvate+Is+a+Metabolic+Checkpoint+of+Anti-tumor+T+Cell+Responses.">Phosphoenolpyruvate Is a Metabolic Checkpoint of Anti-tumor T Cell Responses.</a> Cell. 162 (6), 1217-1228 (2015).</li><li>Chang, C. H., 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=Metabolic+Competition+in+the+Tumor+Microenvironment+Is+a+Driver+of+Cancer+Progression.">Metabolic Competition in the Tumor Microenvironment Is a Driver of Cancer Progression.</a> Cell. 162 (6), 1229-1241 (2015).</li><li>van der Waart, A. B., 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=Inhibition+of+Akt+signaling+promotes+the+generation+of+superior+tumor-reactive+T+cells+for+adoptive+immunotherapy.">Inhibition of Akt signaling promotes the generation of superior tumor-reactive T cells for adoptive immunotherapy.</a> Blood. 124 (23), 3490-3500 (2014).</li><li>Crompton, J. 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=Akt+inhibition+enhances+expansion+of+potent+tumor-specific+lymphocytes+with+memory+cell+characteristics.">Akt inhibition enhances expansion of potent tumor-specific lymphocytes with memory cell characteristics.</a> Cancer Research. 75 (2), 296-305 (2015).</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>Abe, 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=Establishment+of+Conditional+Reporter+Mouse+Lines+at+ROSA26+Locus+For+Live+Cell+Imaging.">Establishment of Conditional Reporter Mouse Lines at ROSA26 Locus For Live Cell Imaging.</a> Genesis. 49 (7), 579-590 (2011).</li><li>Sukumar, 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=Mitochondrial+Membrane+Potential+Identifies+Cells+with+Enhanced+Stemness+for+Cellular+Therapy.">Mitochondrial Membrane Potential Identifies Cells with Enhanced Stemness for Cellular Therapy.</a> Cell Metabolism. 23 (1), 63-76 (2016).</li><li>Sukumar, 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=Inhibiting+glycolytic+metabolism+enhances+CD8++T+cell+memory+and+antitumor+function.">Inhibiting glycolytic metabolism enhances CD8+ T cell memory and antitumor function.</a> Journal of Clinical Investigation. 123 (10), 4479-4488 (2013).</li></ol>

Some elements of this work have been submitted as application P1828EP00 to the European Patent Office.

A tight regulation of HSC function is important to maintain stable hematopoiesis during an organism&#39;s lifetime. Like various other cell types in the body, a key component that contributes to the regulation of HSC function is cellular metabolism. Previous studies from our lab9 and others2,3 have implicated the importance of mitochondria in maintaining a distinct metabolic state in HSCs. Due to the extremely low number of HSCs isolated f...

Hematopoietic stem cells (HSCs) are a small population of cells residing in the bone marrow ensuring blood production and homeostasis throughout an organism&#39;s lifetime. HSCs mediate this process by giving rise to progenitors that in turn produce terminally differentiated mature blood cell lineages via several rounds of cell division and well-orchestrated differentiation steps1. Importantly, HSCs produce their energy via anaerobic glycolysis. In contrast, more committed and active hematopoietic progenitors switch their metabolism toward mitochondrial metabolism2,3,4. This distinct metabolic state is believed to protect the HSCs from cellular damage inflicted by reactive oxygen species (ROS) produced by active mitochondria, thereby maintaining their long-term in vivo function5,6,7,8. Direct measurement of the HSC metabolic state is challenging and often low throughput due to their limited numbers. Here, we describe a flow cytometry-based assay for robust measurement of mitochondrial membrane potential (&#916;&#936;m) using tetramethylrhodamine methyl ester (TMRM) fluorescence, and mitochondrial mass using a green fluorescent mitochondrial stain (Mitotracker Green) in HSCs. We have previously demonstrated that low &#916;&#936;m is a bona-fide functional marker of highly purified HSCs9 and metabolic modulators capable of lowering &#916;&#936;m enhance HSCs function9,10. Here we propose use of our method on HSCs mitochondrial profiling as strategy to identify novel molecules capable of improving the HSCs&#39; long-term blood reconstitution potential.
As an example, we demonstrate that this assay reliably measures the lowering of HSC &#916;&#936;m upon exposure to vitamin B3 analog nicotinamide riboside (NR). Accordingly, in our recently published study we demonstrate that NR strongly ameliorates blood recovery posttransplant in both mouse and humanized mouse systems by directly improving hematopoietic stem and progenitor functions10. The capacity of such metabolic modulators is of great clinical value considering that a 25% death rate is linked to delay in blood and immune recovery in posttransplanted patients11,12.
Moreover, we provide evidence that this methodology can be applied for the characterization of the metabolic profile and function of human T cells. In recent years, the development of adoptive cell therapy (ACT) using autologous tumor infiltrating lymphocytes (TILs) has become the most effective approach for certain types of advanced cancer with extremely unfavorable prognosis (e.g., metastatic melanoma, where &#62;50% of patients respond to treatment and up to 24% of patients have complete regression)13. However, TILs harboring sufficient antitumor activity are difficult to generate14. The extensive proliferation and stimulation that TILs undergo during ex vivo expansion cause T cell exhaustion and senescence that dramatically impair T cell antitumor response15. Importantly, the TILs&#39; antitumoral capacity is tightly linked to their metabolism16,17 and approaches aimed to modulate metabolism through the inhibition of the PI3K/Akt pathway have produced encouraging results18,19. For this reason, we compare the &#916;&#936;m of T cells derived from peripheral blood mononuclear cells (PBMCs) and patient-derived TILs, and show that less differentiated PBMC-derived T cells have lower &#916;&#936;m and mitochondrial mass as compared to terminally differentiated TILs.
We envision that this assay can be used to identify novel metabolic modulators that improve HSC and T cell function via the modulation of &#916;&#936;m.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>5 mL FACS tubes</td>
			<td>Falcon</td>
			<td>352235</td>
			<td>Sample preparation</td>
		</tr>
		<tr>
			<td>96-U bottom plate</td>
			<td>Corning</td>
			<td>3799</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>AutoMACS pro separator</td>
			<td>Miltenyi Biotec</td>
			<td></td>
			<td>Automatic Cell separation</td>
		</tr>
		<tr>
			<td>BD FACS AriaIII</td>
			<td>Becton and Dickinson</td>
			<td></td>
			<td>Cell sorting</td>
		</tr>
		<tr>
			<td>BD IMag mouse hematopoietic progenitor cell enrichment kit</td>
			<td>BD</td>
			<td>558451</td>
			<td>Lineage depletion</td>
		</tr>
		<tr>
			<td>BD LSRII</td>
			<td>Becton and Dickinson</td>
			<td></td>
			<td>FACS acquisition machine</td>
		</tr>
		<tr>
			<td>BD-DIVA</td>
			<td>Becton and Dickinson</td>
			<td></td>
			<td>Acquisition software</td>
		</tr>
		<tr>
			<td>CD150 PE</td>
			<td>Biolegend</td>
			<td>115904</td>
			<td>Antibody staining mix</td>
		</tr>
		<tr>
			<td>CD150 PE-Cy5</td>
			<td>Biolegend</td>
			<td>115912</td>
			<td>Antibody staining mix</td>
		</tr>
		<tr>
			<td>CD48 PB</td>
			<td>Biolegend</td>
			<td>103418</td>
			<td>Antibody staining mix</td>
		</tr>
		<tr>
			<td>Centrifuge- 5810R</td>
			<td>Eppendorf</td>
			<td></td>
			<td>Centrifugation</td>
		</tr>
		<tr>
			<td>Ckit PeCy7</td>
			<td>Biolegend</td>
			<td>105814</td>
			<td>Antibody staining mix</td>
		</tr>
		<tr>
			<td>Flow jo</td>
			<td>FlowJo LLC</td>
			<td></td>
			<td>FACS Analysis software</td>
		</tr>
		<tr>
			<td>GraphPad-Prism</td>
			<td>GraphPad</td>
			<td></td>
			<td>Plotting data into graphs</td>
		</tr>
		<tr>
			<td>Mitotracker Green</td>
			<td>Invitrogen</td>
			<td>M7514</td>
			<td>Green-fluorescent mitocondrial stain to measure mitochondrial mass; working concentration = 100 nM; stock concentration = 1 mM</td>
		</tr>
		<tr>
			<td>Nicotinamide Riboside (NR)</td>
			<td>Custom synthesized in house</td>
			<td></td>
			<td>Metabolic modulator; working concentration = 500 &#181;M; stock concentration = 50 mM</td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>CHUV</td>
			<td>1000324</td>
			<td>Buffer preparation; working concentration = 1x; stock concentration = 1x</td>
		</tr>
		<tr>
			<td>Pen-Strep (P/S)</td>
			<td>Life technologies</td>
			<td>15140122</td>
			<td>Ex vivo culture; working concentration = 1x; stock concentration = 1x</td>
		</tr>
		<tr>
			<td>RBC Lysis buffer</td>
			<td>Biolegend</td>
			<td>420301</td>
			<td>Lysing Red blood cells; working concentration = 1x; stock concentration = 10x</td>
		</tr>
		<tr>
			<td>Recombinant Mouse Flt-3 Ligand (FLT3)</td>
			<td>RnD</td>
			<td>427-FL-005/CF</td>
			<td>Ex vivo culture; working concentration = 2 ng/mL; stock concentration = 10 &#181;g/mL</td>
		</tr>
		<tr>
			<td>Recombinant mouse stem cell factor (SCF)</td>
			<td>RnD</td>
			<td>455-MC-010/CF</td>
			<td>Ex vivo culture; working concentration = 100 ng/mL; stock concentration = 50 &#181;g/mL</td>
		</tr>
		<tr>
			<td>Sca1 APC</td>
			<td>Thermo Fisher Scientific</td>
			<td>17-5981-82</td>
			<td>Antibody staining mix</td>
		</tr>
		<tr>
			<td>StemlineII Hematopoietic Stem Cell Expansion Medium</td>
			<td>SIGMA</td>
			<td>S0192</td>
			<td>Ex vivo culture</td>
		</tr>
		<tr>
			<td>Streptavidin Pac orange</td>
			<td>Life Technologies</td>
			<td>S32365</td>
			<td>Antibody staining mix</td>
		</tr>
		<tr>
			<td>Streptavidin Tx red</td>
			<td>Life Technologies</td>
			<td>S872</td>
			<td>Antibody staining mix</td>
		</tr>
		<tr>
			<td>TMRM</td>
			<td>Invitrogen</td>
			<td>T668</td>
			<td>Staining mitochondrial membrane potential; working concentration = 200 nM; stock concentration = 10 mM</td>
		</tr>
		<tr>
			<td>Ultra pure EDTA</td>
			<td>Invitrogen</td>
			<td>15575-038</td>
			<td>Buffer preparation; working concentration = 0.5 M; stock concentration = 1 mM</td>
		</tr>
	</tbody>
</table>

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.

In Figure 1 we show the gating strategy for the isolation of hematopoietic stem cells from the mouse bone marrow and the layout of the plate for their ex vivo culture. Figure 1A shows the identification of the lymphocyte fraction in the SSC-A/FSC-A plot. Doublets were removed in the singlet gate followed by identification of live cells by the absence of DAPI signal. The LKS population, defined by lineage- Sca1+cKit+, was id...

Watch this Scientific Journal Video about Measurement of Mitochondrial Mass and Membrane Potential in Hematopoietic Stem Cells and T-cells by Flow Cytometry at JoVE.com

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

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 ...

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12.0K Views.  University of Lausanne. Here we describe a reliable method to measure mitochondrial mass and membrane potential in ex vivo cultured hematopoietic stem cells and T cells.

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

Isolation and Transplantation of Hematopoietic Stem Cells (HSCs)

Isolation and Transplantation of Hematopoietic Stem Cells HSCs

I am Christina Ceso. I am a postdoc in David's Den lab and I work on the hematopoietic stem cells. Today we are going to purify long-term recuperating hematopoietic stem cells and we'll transplant them into a mouse.We start by spraying the mice with alcohol so that first of all, the mind starts sterilized and also the hair doesn't interfere with the dissection. We use PBS with 2%serum for the dissection. I cut the back skin and I pull the skin apart in order to expose the tissue.In order to isolate the tibia, I hold the tibia with tweezers. I cut the tendon on top of the knee and I cut the muscles below the knee and after that I cut through the knee so that the TBI is not connected to the rest of the limb anymore and I pull in order to isolate it. I then hold the TB upside down and with the scissors I separate the foot from the tibia In order to obtain the femur.I cut the muscles around the femur and then I dislocate the femur from the hip. In order to isolate the hip, I cut the muscle around the hip bone on the side of the tail of the mouse and then I pull the hip away from the body of the mouth In order to isolate the spine. I cut through the tail as close as I can to the beginning of the back and then I cut on the two sides of the spine and below the spine, trying to stay as close as possible to the spine so that the peritoneum is not cut and the intestine is left untouched.A first round of cleaning of the bones is done with a scalpel, which is used to scrape the bone, the muscles away from the bone. The scalpel is good to clean the femurs, the hip and the spine. In order to clean the tibia, I hold them with forceps and I use the forceps to remove as much tissue as possible.A second round of cleaning is done using clean wipe to completely clean the bones outta the muscle, and I use the F wipe to clean the tibia, the femurs and the hips. So this is how bones look. After cleaning, I prefer 50 amount tubes with filters on top and I transfer the bones into the mortar.I add the section media and I crush the bones ask of the first round of crashing of the bones. I piped the mixture in order to release as many styles as possible into solution and reduce clumps. I transferred the mixture on the tubes through the filters and this is what the bone fragments look like after the first round of crushing.So I add more dissection medium to the bone fragments and I flash them again. I transferred the seline mixture to the tubes through the filters and at this point the remaining bone fragments are white and there is no bone marrow left. The tubes are filled with PBS 2%serum and in order to have them all with the same weight so that they're balanced in the centrifuge, but also in order to wash the filters so that we obtain as many cells as possible, I then centrifuge the cell mixture and after centrifugation, the palt includes the bone marrow cells.I aspirate the medium and I move back and forward the tube on the rack so that the pelle is becomes loose and fewer clamps are formed. When I add medium, at this point I add one ml of medium per tube and I ics since I'm sorting hematopoietic stem cells. Later on, I'm going to store an ALI output of total bone marrow sizes at this point, which I will use later for the fact single color control.I add lineage antibody cocktail. I ordered the samples to mix them well and I invaded four degrees for 15 minutes. In the meantime, I start preparing the columns for the lineage division.I put the columns on the magnet and I prepare Ian tubes under the columns. I also prepared the gas PBS using aster flip filter and attaching it to the vacuum so that all the bubbles of air move in the top part of the filter. I then add three ml of the gas DBS to each column in order for the column to become wet.After the incubation with the antibodies, I add medium to the cell samples and I centrifuge them in order to remove the excess of antibodies. After the centrifugation, the stain cells are in the pallet. I aspirate the medium and I suspend the pallet in one mile of the gas PBSI Add the strip tab beans, I mix the cells and I incubate for 15 minutes at four degrees.After the incubation, I put new elucian tubes under the columns. I add two ml of PBS to each tube with the cells and I transferred the cell mixture to the column through a 40 micron filter. I wash the tubes with more medium in order to collect all the cells remaining and I apply the remaining medium through the filters to the columns.The progenitor cells lineage low are alluded into the collection views. I pulled the luted samples and I sent tofu them. So after the centrifugation, the depleted cells are in a white pate.I aspirate the medium and re suspend the cells. I store an adequate of the depleted cells and I add the antibodies to the cell mixture for the sorting and also to all the single color controls. The antibodies are incubated in that with the size for 15 minutes in the fridge.After the ation, I add medium to the cells and and centrifuge them to remove the ex excess of antibodies. After the centrifugation, the cells are in the pt, I aspirate the media that I suspend the cells and I transfer the cells into fox tubes with a blue filter. At this point, the cells are ready to be sorted.I place, I place the mouse under a heating lamp for a few minutes so that the veins dilate and they are more easily seen. When preparing the syringe, you have to be careful to eliminate all the bubbles from the, the mixture that is in the syringe and then you bend the needle at 90 degrees. I put the mouse under a glass cup with a weight on top so that it can run away.I sterilize the tail with the alcohol pad so that the site of injection is sterile, but also it's easier to identify the vein. If you look at the tail of the mouse from the top in the middle and top of the tail, there is an artery while on the two sides there are the two veins and we inject the cells in one of the two veins. I insert the needle into the vein and I inject following injection.It is to wait for a couple of seconds before removing the needle, the needle, and after that I clean the side of injection. This is a representation of the syringe with the ben needle bent at 90 degrees with the knee, the at this ankle compared to the tail, which makes the injection the easiest. When you injecting the tail of the mouse, you have to keep in mind that the tail vein is extremely superficial, so really this is the orientation of the needle compared to the tail.And it looks like you will just keep sliding on top of the tail, but actually you will get into the tail then. I am Christina Ceso. I am a post in David Kaden lab, and I work on the hematopoietic stem cells.I usually use for animals to start with, and I had more variability at the beginning, but once you become consistent with your methods, I consistently get about 50, 000 to 60, 000 stem cells out for mice. I did my PhD in London with Dr.Fiona Wat working on derma stem cells. After that, I just wanted to have a wider knowledge of adult stem cells in various tissues, and so I decided to move to David Kaden lab to work on hematopoietic stem cells, mainly because the things that are known about hematopoietic stem cells are the things that are not known for the epidermic stem cells and a number of assays that can be done with epi.Epidermal stem cells are not really done yet with the hematopoietic stem cells, and so at this point I'm trying to put together the, the knowledge from the two different fields and ultimately I'm interested in the study of the mechanism to regulate adult tissue sensors in general, so not just the epidermis or the stem cells, but also different tissues because there are, there are similar mechanism that is, it's always the same genes that are involved in the regulation that just interact with each other in different ways, and it's just interesting to understand what makes each stem cell be a stem, but then ultimately a stem cell in a different tissue. So giving rise to a different protein.

Quantitative Measurement of GLUT4 Translocation to the Plasma Membrane by Flow Cytometry

Glucose is the main source of energy for the body, requiring constant regulation of its blood concentration. Insulin release by the pancreas induces glucose uptake by insulin-sensitive tissues, most notably the brain, skeletal muscle, and adipocytes. Patients suffering from type-2 diabetes and/or obesity often develop insulin resistance and are unable to control their glucose homeostasis. New insights into the mechanisms of insulin resistance may provide new treatment strategies for type-2 diabetes.
The GLUT family of glucose transporters consists of thirteen members distributed on different tissues throughout the body1. Glucose transporter type 4 (GLUT4) is the major transporter that mediates glucose uptake by insulin sensitive tissues, such as the skeletal muscle. Upon binding of insulin to its receptor, vesicles containing GLUT4 translocate from the cytoplasm to the plasma membrane, inducing glucose uptake. Reduced GLUT4 translocation is one of the causes of insulin resistance in type-2 diabetes2,3.
The translocation of GLUT4 from the cytoplasm to the plasma membrane can be visualized by immunocytochemistry, using fluorophore-conjugated GLUT4-specific antibodies.
Here, we describe a technique to quantify total amounts of GLUT4 translocation to the plasma membrane of cells during a chosen duration, using flow cytometry. This protocol is rapid (less than 4 hours, including incubation with insulin) and allows the analysis of as few as 3,000 cells or as many as 1 million cells per condition in a single experiment. It relies on anti-GLUT4 antibodies directed to an external epitope of the transporter that bind to it as soon as it is exposed to the extracellular medium after translocation to the plasma membrane.

This protocol describes a rapid technique to quantify the translocation of GLUT4 from the cytoplasm to the plasma membrane of cells by flow cytometry.

Glucose is the main source of energy for the body, requiring constant regulation of its blood concentration. Insulin release by the pancreas induces ...

Phenotypic Analysis and Isolation of Murine Hematopoietic Stem Cells and Lineage-committed Progenitors

The bone marrow is the principal site where HSCs and more mature blood cells lineage progenitors reside and differentiate in an adult organism. HSCs constitute a minute cell population of pluripotent cells capable of generating all blood cell lineages for a life-time1. The molecular dissection of HSCs homeostasis in the bone marrow has important implications in hematopoiesis, oncology and regenerative medicine. We describe the labeling protocol with fluorescent antibodies and the electronic gating procedure in flow cytometry to score hematopoietic progenitor subsets and HSCs distribution in individual mice (Fig. 1). In addition, we describe a method to extensively enrich hematopoietic progenitors as well as long-term (LT) and short term (ST) reconstituting HSCs from pooled bone marrow cell suspensions by magnetic enrichment of cells expressing c-Kit. The resulting cell preparation can be used to sort selected subsets for in vitro and in vivo functional studies (Fig. 2).
Both trabecular osteoblasts2,3 and sinusoidal endothelium4 constitute functional niches supporting HSCs in the bone marrow. Several mechanisms in the osteoblastic niche, including a subset of N-cadherin+ osteoblasts3 and interaction of the receptor tyrosine kinase Tie2 expressed in HSCs with its ligand angiopoietin-15 concur in determining HSCs quiescence. "Hibernation" in the bone marrow is crucial to protect HSCs from replication and eventual exhaustion upon excessive cycling activity6. Exogenous stimuli acting on cells of the innate immune system such as Toll-like receptor ligands7 and interferon-&alpha;6 can also induce proliferation and differentiation of HSCs into lineage committed progenitors. Recently, a population of dormant mouse HSCs within the lin- c-Kit+ Sca-1+ CD150+ CD48- CD34- population has been described8. Sorting of cells based on CD34 expression from the hematopoietic progenitors-enriched cell suspension as described here allows the isolation of both quiescent self-renewing LT-HSCs and ST-HSCs9. A similar procedure based on depletion of lineage positive cells and sorting of LT-HSC with CD48 and Flk2 antibodies has been previously described10. In the present report we provide a protocol for the phenotypic characterization and ex vivo cell cycle analysis of hematopoietic progenitors, which can be useful for monitoring hematopoiesis in different physiological and pathological conditions. Moreover, we describe a FACS sorting procedure for HSCs, which can be used to define factors and mechanisms regulating their self-renewal, expansion and differentiation in cell biology and signal transduction assays as well as for transplantation.

A method to analyse the distribution of bone marrow hematopoietic progenitors in flow cytometry as well as to efficiently isolate highly purified hematopoietic stem cells (HSCs) is described. The isolation procedure is essentially based on magnetic enrichment of c-Kit+ cells and cell sorting to purify HSCs for cellular and molecular studies.

The bone marrow is the principal site where HSCs and more mature blood cells lineage progenitors reside and differentiate in an adult organism. HSCs ...

Optimized Staining and Proliferation Modeling Methods for Cell Division Monitoring using Cell Tracking Dyes

Fluorescent cell tracking dyes, in combination with flow and image cytometry, are powerful tools with which to study the interactions and fates of different cell types in vitro and in vivo.1-5 Although there are literally thousands of publications using such dyes, some of the most commonly encountered cell tracking applications include monitoring of:
<ol>
	<li>stem and progenitor cell quiescence, proliferation and/or differentiation6-8</li>
	<li>antigen-driven membrane transfer9 and/or precursor cell proliferation3,4,10-18 and</li>
	<li>immune regulatory and effector cell function1,18-21.</li>
</ol>
Commercially available cell tracking dyes vary widely in their chemistries and fluorescence properties but the great majority fall into one of two classes based on their mechanism of cell labeling. "Membrane dyes", typified by PKH26, are highly lipophilic dyes that partition stably but non-covalently into cell membranes1,2,11. "Protein dyes", typified by CFSE, are amino-reactive dyes that form stable covalent bonds with cell proteins4,16,18. Each class has its own advantages and limitations. The key to their successful use, particularly in multicolor studies where multiple dyes are used to track different cell types, is therefore to understand the critical issues enabling optimal use of each class2-4,16,18,24.
The protocols included here highlight three common causes of poor or variable results when using cell-tracking dyes. These are:
<ol>
	<li>Failure to achieve bright, uniform, reproducible labeling. This is a necessary starting point for any cell tracking study but requires attention to different variables when using membrane dyes than when using protein dyes or equilibrium binding reagents such as antibodies.</li>
	<li>Suboptimal fluorochrome combinations and/or failure to include critical compensation controls. Tracking dye fluorescence is typically 102 - 103 times brighter than antibody fluorescence. It is therefore essential to verify that the presence of tracking dye does not compromise the ability to detect other probes being used.</li>
	<li>Failure to obtain a good fit with peak modeling software. Such software allows quantitative comparison of proliferative responses across different populations or stimuli based on precursor frequency or other metrics. Obtaining a good fit, however, requires exclusion of dead/dying cells that can distort dye dilution profiles and matching of the assumptions underlying the model with characteristics of the observed dye dilution profile.</li>
</ol>
Examples given here illustrate how these variables can affect results when using membrane and/or protein dyes to monitor cell proliferation.

Successful use of cell tracking dyes to monitor immune cell function and proliferation involves several critical steps. We describe methods for: 1) obtaining bright, uniform, reproducible label-ing with membrane dyes; 2) selecting fluorochromes and data acquisition conditions; and 3) choosing a model to quantify cell proliferation based on dye dilution.

Fluorescent cell tracking dyes, in combination with flow and image cytometry, are powerful tools with which to study the interactions and fates of ...

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) ...

Cytosolic Calcium Measurements in Renal Epithelial Cells by Flow Cytometry

A variety of cellular processes, both physiological and pathophysiological, require or are governed by calcium, including exocytosis, mitochondrial function, cell death, cell metabolism and cell migration to name but a few. Cytosolic calcium is normally maintained at low nanomolar concentrations; rather it is found in high micromolar to millimolar concentrations in the endoplasmic reticulum, mitochondrial matrix and the extracellular compartment. Upon stimulation, a transient increase in cytosolic calcium serves to signal downstream events. Detecting changes in cytosolic calcium is normally performed using a live cell imaging set up with calcium binding dyes that exhibit either an increase in fluorescence intensity or a shift in the emission wavelength upon calcium binding. However, a live cell imaging set up is not freely accessible to all researchers. Alternative detection methods have been optimized for immunological cells with flow cytometry and for non-immunological adherent cells with a fluorescence microplate reader. Here, we describe an optimized, simple method for detecting changes in epithelial cells with flow cytometry using a single wavelength calcium binding dye. Adherent renal proximal tubule epithelial cells, which are normally difficult to load with dyes, were loaded with a fluorescent cell permeable calcium binding dye in the presence of probenecid, brought into suspension and calcium signals were monitored before and after addition of thapsigargin, tunicamycin and ionomycin.

Calcium is involved in numerous physiological and pathophysiological signaling pathways. Live cell imaging requires specialized equipment and can be time consuming. A quick, simple method using a flow cytometer to determine relative changes in cytosolic calcium in adherent epithelial cells brought into suspension was optimized.

A variety of cellular processes, both physiological and pathophysiological, require or are governed by calcium, including exocytosis, mitochondrial ...

High Efficiency Differentiation of Human Pluripotent Stem Cells to Cardiomyocytes and Characterization by Flow Cytometry

There is an urgent need to develop approaches for repairing the damaged heart, discovering new therapeutic drugs that do not have toxic effects on the heart, and improving strategies to accurately model heart disease. The potential of exploiting human induced pluripotent stem cell (hiPSC) technology to generate cardiac muscle &#8220;in a dish&#8221; for these applications continues to generate high enthusiasm. In recent years, the ability to efficiently generate cardiomyogenic cells from human pluripotent stem cells (hPSCs) has greatly improved, offering us new opportunities to model very early stages of human cardiac development not otherwise accessible. In contrast to many previous methods, the cardiomyocyte differentiation protocol described here does not require cell aggregation or the addition of Activin A or BMP4 and robustly generates cultures of cells that are highly positive for cardiac troponin I and T (TNNI3, TNNT2), iroquois-class homeodomain protein IRX-4 (IRX4), myosin regulatory light chain 2, ventricular/cardiac muscle isoform (MLC2v) and myosin regulatory light chain 2, atrial isoform (MLC2a) by day 10 across all human embryonic stem cell (hESC) and hiPSC lines tested to date. Cells can be passaged and maintained for more than 90 days in culture. The strategy is technically simple to implement and cost-effective. Characterization of cardiomyocytes derived from pluripotent cells often includes the analysis of reference markers, both at the mRNA and protein level. For protein analysis, flow cytometry is a powerful analytical tool for assessing quality of cells in culture and determining subpopulation homogeneity. However, technical variation in sample preparation can significantly affect quality of flow cytometry data. Thus, standardization of staining protocols should facilitate comparisons among various differentiation strategies. Accordingly, optimized staining protocols for the analysis of IRX4, MLC2v, MLC2a, TNNI3, and TNNT2 by flow cytometry are described.

The article describes the detailed methodology to efficiently differentiate human pluripotent stem cells into cardiomyocytes by selectively modulating the Wnt pathway, followed by flow cytometry analysis of reference markers to assess homogeneity and identity of the population.

There is an urgent need to develop approaches for repairing the damaged heart, discovering new therapeutic drugs that do not have toxic effects on the ...

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+ ...

Analysis of Cell Suspensions Isolated from Solid Tissues by Spectral Flow Cytometry

Flow cytometry has been used for the past 40 years to define and analyze the phenotype of lymphoid and other hematopoietic cells. Initially restricted to the analysis of a few fluorochromes, currently there are dozens of different fluorescent dyes, and up to 14-18 different dyes can be combined at a time. However, several limitations still impair the analytical capabilities. Because of the multiplicity of fluorescent probes, data analysis has become increasingly complex due to the need of large, multi-parametric compensation matrices. Moreover, mutant mouse models carrying fluorescent proteins to detect and trace specific cell types in different tissues have become available, so the analysis (by flow cytometry) of auto-fluorescent cell suspensions obtained from solid organs is required. Spectral flow cytometry, which distinguishes the shapes of emission spectra along a wide range of continuous wavelengths, addresses some of these problems. The data is analyzed with an algorithm that replaces compensation matrices and treats auto-fluorescence as an independent parameter. Thus, spectral flow cytometry should be capable of discriminating fluorochromes with similar emission peaks and can provide a multi-parametric analysis without compensation requirements.
This protocol describes the spectral flow cytometry analysis, allowing for a 21-parameter (19 fluorescent probes) characterization and the management of an auto-fluorescent signal, providing high resolution in minor population detection. The results presented here show that spectral flow cytometry presents advantages in the analysis of cell populations from tissues difficult to characterize in conventional flow cytometry, such as the heart and the intestine. Spectral flow cytometry thus demonstrates the multi-parametric analytical capacity of high-performing conventional flow cytometry without the requirement for compensation and enables auto-fluorescence management.

This article describes spectral cytometry, a new approach in flow cytometry that uses the shapes of emission spectra to distinguish fluorochromes. An algorithm replaces compensations and can treat auto-fluorescence as an independent parameter. This new approach allows for the proper analysis of cells isolated from solid organs.

Flow cytometry has been used for the past 40 years to define and analyze the phenotype of lymphoid and other hematopoietic cells. Initially restricted to ...

High-throughput Measurement of Dictyostelium discoideum Macropinocytosis by Flow Cytometry

Large-scale non-specific fluid uptake by macropinocytosis is important for the proliferation of certain cancer cells, antigen sampling, host cell invasion and the spread of neurodegenerative diseases. The commonly used laboratory strains of the amoeba Dictyostelium discoideum have extremely high fluid uptake rates when grown in nutrient medium, over 90% of which is due to macropinocytosis. In addition, many of the known core components of mammalian macropinocytosis are also present, making it an excellent model system for studying macropinocytosis. Here, the standard technique to measure internalized fluid using fluorescent dextran as a label is adapted to a 96-well plate format, with the samples analyzed by flow cytometry using a high-throughput sampling (HTS) attachment.
Cells are fed non-quenchable fluorescent dextran for a pre-determined length of time, washed by immersion in ice-cold buffer and detached using 5 mM sodium azide, which also stops exocytosis. Cells in each well are then analyzed by flow cytometry. The method can also be adapted to measure membrane uptake and phagocytosis of fluorescent beads or bacteria.
This method was designed to allow measurement of fluid uptake by Dictyostelium in a high-throughput, labor and resource efficient manner. It allows simultaneous comparison of multiple strains (e.g. knockout mutants of a gene) and conditions (e.g. cells in different media or treated with different concentrations of inhibitor) in parallel and simplifies time-courses.

High-throughput Measurement of Dictyostelium discoideum Macropinocytosis by Flow Cytometry

Macropinocytosis, large-scale non-specific fluid uptake, is important in many areas of clinical biology including immunology, infection, cancer, and neurodegenerative diseases. Here, existing techniques have been adapted to allow high-throughput, single-cell resolution measurement of macropinocytosis in the macropinocytosis model organism Dictyostelium discoideum using flow cytometry.

Large-scale non-specific fluid uptake by macropinocytosis is important for the proliferation of certain cancer cells, antigen sampling, host cell invasion ...