This work was supported by the Intramural Research Program of the National Heart, Lung, Blood Institute of the National Institutes of Health. We thank Boris Fehse (University Medical Center Hamburg-Eppendorf, Hamburg, Germany) for providing the five LeGO vector plasmids; Christian A. Combs and Neal S. Young (NHLBI, NIH) for discussions, support and encouragement throughout this study, and Andre LaRochelle (NHLBI, NIH) for assistance with tail vein injections.

All mice were housed and handled in accordance with the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health, and enrolled in an NHLBI Animal Care and Use Committee&#8211;approved protocol. Female B6.SJL-Ptprc(d)Pep3(b)/BoyJ (B6.SJL) and C57Bl/6 mice, 6-12 weeks old, were used as donor and recipient, respectively.
A list of materials, reagents, and equipment is provided in Table 1.
1. LeGO Transduction of Mouse HSPCs and Bone Marrow Transplantation
Perform procedures described below in a certified biosafety level 2 (BSL-2) cabinet (tissue culture hood).
<ol>
	<li>Production of LeGO Vectors Encoding 5FPs
	<ol>
		<li>Use the lentiviral &#8220;Gene Ontology&#8221; (LeGO) vector plasmids, each encoding a different FP from a strong constitutive SFFV promoter, including LeGO-Cer2 (Cerulean), LeGO-G2 (EGFP), LeGO-V2 (Venus), LeGO-T2 (tdTomato), and LeGO-C2 (mCherry) kindly provided by Dr. Boris Fehse (University Medical Center Hamburg-Eppendorf, Hamburg, Germany); now also available from Addgene5-7.</li>
		<li>To produce LeGO vectors, seed 5 x 106 293T cells in 10 cm dishes (use 12 dishes for each vector) 24 hr prior to transfection in 8 ml of I10 media (IMDM supplemented with 10% FCS and glutamine /penicillin /streptomycin).</li>
		<li>Transfect the cells with Calcium Phosphate using slightly modified CAPHOS kit recommendations:
		<ol>
			<li>For each plate mix 15 &#181;g LeGO vector, 12 &#181;g pCDNA3.HIVgag/pol.4xCTE, 4 &#181;g pRev-TAT, and 1 &#181;g pMD2.G-VSV-G plasmids in presence of 50 &#181;l&#160;2.5 M CaCl2, and add water to yield a 500 &#181;l&#160;total volume.</li>
			<li>Precipitate DNA plasmids with 500 &#181;l&#160;of 2x HeBS (HEPES-Buffered Saline) and incubate for 20 min at room temperature prior to adding to each plate of 293T cells.</li>
			<li>Incubate cells for 6 hr in a 37 &#176;C 5% CO2 incubator; remove media and add fresh culture media 6 hr post transfection.</li>
		</ol>
		</li>
		<li>Collect culture supernatants containing lentiviral particles from each plate, daily, for 3 days. Each day following supernatant collection add fresh I10 media to each plate.
		<ol>
			<li>Filter through 0.22 &#181;m pores, pool and concentrate supernatants by ultracentrifugation on an SW28 rotor for 2 hr at 71,900 x g and 4&#160;&#176;C.</li>
			<li>Resuspend the supernatants in 1 ml of StemSpan media. Aliquot the lentiviral stocks in 200 &#181;l&#160;and store at -80 &#176;C.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Titration of Lentiviral Particles 
	Determine the titer of LeGO vector particles in collected supernatants via quantitation of transducing units/ml using NIH3T3 cells. Titers allow calculation of the volume of each vector supernatant needed to result in the desired relative multiplicity of infection (MOI) for experimental target cells.
	<ol>
		<li>Plate 5 x 104 NIH3T3 cells per well (12-well plate) in 2 ml of I10 media one day before the titration.</li>
		<li>Prepare 5-fold serial dilutions of vector supernatants in I10 media supplemented with protamine sulfate (4 mg/ml&#160;is 1,000x).</li>
		<li>Remove the media from the cells, and replace with 500 &#181;l of supernatant dilutions containing the equivalent of 2, 0.8, 0.32, and 0.128 &#181;l of concentrated virus.</li>
		<li>Determine the number (No) of cells present per well at the time of transduction, counting one control well.</li>
		<li>6 hr after transduction, add 2 ml of I10 media and incubate for 3 days at 37 &#176;C, 5% CO2.</li>
		<li>Harvest the cells from each well using Trypsin-EDTA, and determine the percentage of fluorescent cells (%FP) via flow cytometry.</li>
		<li>Calculate the titer as follow, averaging the titers obtained for each well (dilution) resulting in a %FP between 1 and 50%: Titer (vector particles/ml) = No x %FP/ Volume of vector supernatant (ml). Average the titers obtained for each dilution if the %FP is between 1 and 50%.</li>
	</ol>
	</li>
	<li>Mouse Cell Collection, Purification, Transduction, and Transplantation (schematically shown in Figure 1A adapted from Malide et al.4).
	<ol>
		<li>Sacrifice donor mice by an approved procedure. Harvest bone marrow from anterior and posterior limbs: dissect humeri, femurs and tibias, thoroughly remove all muscle, ligaments and excess tissue from bones, cut across the end of each bone as close as possible to the joint, and flush the bone marrow out of the bone using a 27-0 G&#160;needle on a syringe containing I10 media.</li>
		<li>Pellet the whole bone marrow cells for 10 min at 500 x g, 4 &#176;C and lyse red cells twice with 50 ml ACK buffer. Resuspend cells in 10 ml I10 media.</li>
		<li>Purify lineage negative (Lin-) progenitor cells with the MACS lineage depletion kit according to a modified kit protocol:
		<ol>
			<li>Use 30 &#181;l of Anti-Biotin MicroBeads instead of 10 &#181;l/ 107 cells; complete the washing steps with I2 media (IMDM supplemented with 2% FCS) instead of buffer.</li>
			<li>Insert one washing step between the incubation with Biotin-Antibody Cocktail and the incubation with Anti-Biotin MicroBeads; and equilibrate the column with I10 instead of buffer.</li>
		</ol>
		</li>
		<li>Culture Lin- cells for 48 hr at a starting density of 5 x 105 cells/ml in StemSpan media supplemented with 10 ng/ml murine IL-3, 100 ng/ml murine IL-11, 100 ng/ml human Flt-3 ligand, and 50 ng/ml murine stem cell factor.</li>
		<li>Transfer 1 to 4 x 105 cells to 12-well plates coated with RetroNectin and transduce with LeGO supernatants, each at a multiplicity of infection (MOI) of 6-7 to achieve 50% expression efficiency for each FP, in the presence of StemSpan media and cytokines detailed above and 4 &#181;g/ml protamine sulfate.</li>
		<li>Transduce cells with each LeGO vector individually as described in step 1.3.5 and mix cells following transduction (termed Mix) or co-transduce cells with all 5 LeGO vector supernatants simultaneously (termed Co). Remove cells 24 hr later, wash once with StemSpan media without cytokines, and resuspend them in StemSpan media without cytokines for transplantation, or transfer them to fresh media with cytokines, and culture for additional 96 hr before confocal microscopy and flow cytometry.
		<ol>
			<li>Perform bone marrow transplant by infusing transduced Lin- HSPCs via tail vein injection into 11 Gy single dose pre-irradiated recipients (6-18 hr&#160;prior to transplant)&#160;recipients, in a volume of 100 &#181;l, at a cell dose per mouse corresponding to 1-4 x 105 Lin- cells originally plated for transduction. In each experiment, transplant an entire cohort of animals with the same population of transduced donor BM cells.</li>
			<li>For in vitro characterization of transduced HSPCs, culture the cells for an additional 4-5 days in StemSpan supplemented with cytokines and analyze by flow cytometry for transduction efficiency, and by microscopy for color diversity.
			<ol>
				<li>Sacrifice individual mice&#160;and retrieve tissues and organs for imaging, at various time points up to 120 days post-transplantation.
				<ol>
					<li>Spray with&#160;ethanol the fur of the mouse and incise the skin on the ventral side avoiding hair dissemination.</li>
					<li>Dissect and excise according to standard procedures the spleen, popliteal lymph nodes, lung, heart, skin, adipose tissue, skeletal muscle, kidney, liver, as well as the head to access to calvaria.</li>
					<li>Alternatively, use calvaria or set up a bone window for live imaging repeatedly over time2,8,9 or image superficial organs such as the skin and lymph nodes in the live animal.</li>
				</ol>
				</li>
				<li>Place individual organs in 35 mm number 0 cover glass culture dishes in 50-100 &#956;l PBS&#160;for imaging them intact without sectioning, fixation or further processing as described in step 2.5.</li>
				<li>For volumetric imaging, keep the organs in in cold PBS until use. For time-lapse imaging proceed immediately to imaging organs in DMEM, 10% FBS containing 20 mM HEPES at 37 &#176;C</li>
			</ol>
			</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
2. Confocal and Two-photon Microscopy and Image Analysis
<ol>
	<li>Perform microscopy imaging using a Leica SP5 five channels confocal and multiphoton system equipped with multi-line Argon, diode 561 nm, HeNe 594 nm, and HeNe 633 nm visible lasers. Use in 2-photon mode, a pulsed femtosecond Ti:Sapphire (Ti-Sa) laser, tunable for excitation from 680 to 1,080 nm with dispersion correction. Use in experiments involving red-shifted FPs (tdTomato and mCherry), an optical parametric oscillator (OPO) laser to extend the output wavelength range as far as 1,030-1,300 nm, sequentially or simultaneously with the Ti-Sa laser.</li>
	<li>Image various tissues using a HCX-IRAPO-L 25X/0.95 NA water dipping objective (WD = 2.5 mm), a HC-PLAPO-CS 20X/0.70 NA dry objective (WD = 0.6 mm), or HC-PL-IRAPO 40X/1.1 NA water immersion objective (WD = 0.6 mm).</li>
	<li>Obtain confocal fluorescence spectra collecting lambda stacks (xy&#955;) of emitted light in 5 nm-bandwidths of the visible spectrum from BM cells transduced with a single FP LeGO vector as well as of control, not-transplanted BM.
	<ol>
		<li>Process images with the Leica LAS-AF v2.4.1 software to create reference spectra of all 5 FPs as well as of autofluorescence (Figure 2A). Using the individual FP spectra and the difference in fluorescence brightness (expressed as % of EGFP) of Cerulean (79%), Venus (156%), tdTomato (283%) and mCherry (47%) set 5 sequential imaging channels as follows: Cerulean (458/468-482 nm), EGFP (488/496-514 nm), Venus (514/523-558 nm), tdTomato (561/579-597 nm), and mCherry (594/618-670 nm) (Figure 2B).</li>
		<li>Validate accurate FPs separation, as cells transduced with each individual FP are visible only in the corresponding channel and absent from the rest (Figure 2C). In addition, this defined multi-channel approach creates an unique 5-channels &#8220;colorprint&#8221; that enables subsequent color analysis and clonal tracking and has the advantage of reducing acquisition times compared to spectral imaging.</li>
	</ol>
	</li>
	<li>Separate fluorescence emission, in 2-photon mode, by high-efficiency custom dichroic mirrors and collect with a four channels non-descanned detector (NDD) as follows: a dichroic mirror at 568 nm followed by a dichroic mirror at 465 nm, followed by a 452/45 nm emission filter for SHG or autofluorescence and Cerulean, a 525/40 nm emission filter for EGFP or Venus, and a 648 nm dichroic mirror and 620/60 nm emission filter for tdTomato or mCherry.
	<ol>
		<li>Reveal structural information by two-photon microscopy intrinsic contrast imaging (as described above) of tissue autofluorescence from elastin, NADH, (excited at 780 nm), and second harmonic generated signal (SHG) from bone and fibrillar collagen (excited at 920 nm or 860 nm collected in a back-scattered direction)10,11.</li>
	</ol>
	</li>
	<li>For 3D volume rendering, collect series of x-y-z images (typically 1 x&#160;1 x&#160;4 &#956;m3&#160;voxel size) along the z-axis at 5 &#956;m intervals over a range of depths (150-300 &#956;m) throughout the bone marrow and other tissues, over large regions using the tile function of the software to automatically generate stitched volumes comprising an entire sternum fossae, approximately 2.5 x&#160;1.2 mm2 (x-y) and 300 &#956;m (z) (Figures 2D-2E) and Movie&#160;1.
	<ol>
		<li>Image calvarial marrow directly through the skull without sectioning2, 8.</li>
		<li>Section sternum along the sagittal plane (bisection) and then transversally at the joint between 2 sternal fosse and image through the cut face3,4,12 (Overview in Figure 1B adapted from Takaku et al3).</li>
	</ol>
	</li>
	<li>For 4D time-lapse imaging, place freshly excised popliteal lymph node, spleen, lung, or calvarial bone samples uncut onto 35 mm number 0 coverglass culture dishes, in 50-100 &#956;l&#160;DMEM, 10% FBS containing 20 mM HEPES at 37 &#176;C and use 2-photon Ti-Sa excitation (860 nm) combined with confocal excitation (458 nm, 488 nm, 514 nm, 561 nm, 594 nm) and Leica resonant scanner (8000 Hz/sec), taking z-stacks (~80 &#956;m) at 20 sec intervals for up to 1 hr.
	<ol>
		<li>For simultaneous three-color 2P imaging use Ti-Sa tuned at 860 nm simultaneously with the OPO laser (tuned at 1,130 nm&#160;for tdTomato; or 1,140 nm mCherry) (Movie&#160;2).</li>
	</ol>
	</li>
	<li>Reconstruction and Analysis of 3D Volumes and 4D time sequences
	<ol>
		<li>Use Imaris x64 software version 7.6, or alternative software packages to transform the tiled-stacks of raw images into volume-rendered (3D) data of fluorescent cells inside bone marrow and different tissues and to export them as 3D-rotation movies, as previously described3,4 (Movie&#160;1) step-by-step example:
		<ol>
			<li>In Imaris, Open the z-stack image; Select &#8220;Surpass&#8221; in order to display the 3D volume visualization.</li>
			<li>Use &#8220;navigate&#8221; to turn the volume around 360&#176;.</li>
			<li>Select &#8220;Animation&#8221; to create an animation; use key frames to add selected views, zoom, rotations of the volume; Preview the movie, edit as necessary and save the file in a desired movie format (ex: avi, mov).</li>
		</ol>
		</li>
		<li>For quantitative assessment of the 3D cell and clone frequency, positions, sizes and distribution, further process the z-stacks using the Imaris XT modules which integrate MATLAB applications performing distance measurements (using a distance transformation algorithm) and clusters analysis, as previously described3,4. Transform the sequences of image stacks over time into volume-rendered four-dimensional (4D) movies with Imaris x64 software, and use spot and surface analysis for semiautomated tracking of cell motility in three dimensions using autoregressive motion algorithms.</li>
		<li>Perform multispectral analysis of cells as follows: extract the multi-color labeled spots by adding all 5 channels through channel arithmetic of Imaris XT into a new channel; determine for all spots (cells) the mean intensity fluorescence in each of the 5 component channels. Export the values in Excel software to plot graphs displaying the unique&#8221; colorprint&#8221; i.e. the relative % of each FP in individual cell (Figure 2E graph). Correct the data set for tissue drift, and calculate cell velocity and displacement over time, track lengths, paths, and distances; export values in Excel software to plot graphs. Assemble composite figures with Adobe Photoshop CSS 5 software.</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Lo Celso, ., C, D. T., Scadden, <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+haematopoietic+stem+cell+niche+at+a+glance.">The haematopoietic stem cell niche at a glance.</a> J Cell Sci. 124, 3529-3535 (2011).</li><li>Lo Celso, 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=Live-animal+tracking+of+individual+haematopoietic+stem/progenitor+cells+in+their+niche.">Live-animal tracking of individual haematopoietic stem/progenitor cells in their niche.</a> Nature. 457, 92-96 (2009).</li><li>Takaku, 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=Hematopoiesis+in+3+dimensions+human+and+murine+bone+marrow+architecture+visualized+by+confocal+microscopy.">Hematopoiesis in 3 dimensions human and murine bone marrow architecture visualized by confocal microscopy.</a> Blood. 116, e41-e55 (2010).</li><li>Malide, D., Metais, J. Y., Dunbar, C. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamic+clonal+analysis+of+murine+hematopoietic+stem+and+progenitor+cells+marked+by+5+fluorescent+proteins+using+confocal+and+multiphoton+microscopy.">Dynamic clonal analysis of murine hematopoietic stem and progenitor cells marked by 5 fluorescent proteins using confocal and multiphoton microscopy.</a> Blood. 120, e105-e116 (2012).</li><li>Weber, K., Mock, U., Petrowitz, B., Bartsch, U., Fehse, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lentiviral+gene+ontology+(LeGO)+vectors+equipped+with+novel+drug-selectable+fluorescent+proteins+new+building+blocks+for+cell+marking+and+multi-gene+analysis.">Lentiviral gene ontology (LeGO) vectors equipped with novel drug-selectable fluorescent proteins new building blocks for cell marking and multi-gene analysis.</a> Gene Ther. 17, 511-520 (2010).</li><li>Weber, K., Bartsch, U., Stocking, C., Fehse, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+multicolor+panel+of+novel+lentiviral+'gene+ontology'+(LeGO)+vectors+for+functional+gene+analysis.">A multicolor panel of novel lentiviral 'gene ontology' (LeGO) vectors for functional gene analysis.</a> Mol Ther. 16, 698-706 (2008).</li><li>Weber, 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=RGB+marking+facilitates+multicolor+clonal+cell+tracking.">RGB marking facilitates multicolor clonal cell tracking.</a> Nat Med. 17, 504-509 (2011).</li><li>Lo Celso, ., Lin, C. P., 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=In+vivo+imaging+of+transplanted+hematopoietic+stem+and+progenitor+cells+in+mouse+calvarium+bone+marrow.">In vivo imaging of transplanted hematopoietic stem and progenitor cells in mouse calvarium bone marrow.</a> Nature protocols. 6, 1-14 (2011).</li><li>Kohler, 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=Altered+cellular+dynamics+and+endosteal+location+of+aged+early+hematopoietic+progenitor+cells+revealed+by+time-lapse+intravital+imaging+in+long+bones.">Altered cellular dynamics and endosteal location of aged early hematopoietic progenitor cells revealed by time-lapse intravital imaging in long bones.</a> Blood. 114, 290-298 (2009).</li><li>Campagnola, P. 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The authors declare no competing financial interests.

We describe here the details of a powerful methodology recently devised for clonal cell tracking, combining the large diversity generated by combinatorial marking with 5FP-encoding LeGO vectors and imaging with tandem confocal and 2-photon microscopy to achieve volumetric and dynamic imaging in live tissues. This extended the use of FP-based color marking by recording confocal spectral identity in 5 &#8220;distinct&#8221; 8-bits channels. Thus the relative ratio of Cerulean, EGFP, Venus, tdTomato, mCherry within each cel...

A correction was made to <a href="/video/51669">In vivo Clonal Tracking of Hematopoietic Stem and Progenitor Cells Marked by Five Fluorescent Proteins using Confocal and Multiphoton Microscopy</a>. At the time of publication, there was a typo in the discussion, which displayed an incorrect depth.
This was corrected in the discussion from:
This approach combines the benefits of single-cell resolved high resolution imaging together with optical sectioning via confocal microscopy. Very large x - y (mm2) regions of the intact dense tissue volume can be examined by generating tiled-images. These high resolution images from optical sections can be used to computationally reconstruct (automatically and &#8220;on-the-fly&#8221;) complete 3D volumes of great complexity to depths of ~ 30 &#956;m, comprising ~ 20-30 layers of cells, vascular, bone and collagen structures. 3D reconstructions can be used for morphometric non-invasive quantitative analyses of biologic interest. One important caveat to point out is that large volume/high resolution imaging is time-consuming, for instance 1 hr per ~1 mm3 of tissue (one fossae of the sternum), therefore we recommend imaging no more than 1 mouse per experiment per day when bone marrow as well as different tissues need to be examined in detail.
to:
This approach combines the benefits of single-cell resolved high resolution imaging together with optical sectioning via confocal microscopy. Very large x - y (mm2) regions of the intact dense tissue volume can be examined by generating tiled-images. These high resolution images from optical sections can be used to computationally reconstruct (automatically and &#8220;on-the-fly&#8221;) complete 3D volumes of great complexity to depths of ~ 300 &#956;m, comprising ~ 20-30 layers of cells, vascular, bone and collagen structures. 3D reconstructions can be used for morphometric non-invasive quantitative analyses of biologic interest. One important caveat to point out is that large volume/high resolution imaging is time-consuming, for instance 1 hr per ~1 mm3 of tissue (one fossae of the sternum), therefore we recommend imaging no more than 1 mouse per experiment per day when bone marrow as well as different tissues need to be examined in detail.

A correction was made to <a href="/video/51669">In vivo Clonal Tracking of Hematopoietic Stem and Progenitor Cells Marked by Five Fluorescent Proteins using Confocal and Multiphoton Microscopy</a>. At the time of publication, there was a typo in the discussion, which displayed an incorrect depth.

Erratum: In vivo Clonal Tracking of Hematopoietic Stem and Progenitor Cells Marked by Five Fluorescent Proteins using Confocal and Multiphoton Microscopy

The production of blood cells, termed hematopoiesis, is maintained by a small population of hematopoietic stem and progenitor cells (HSPCs). These cells reside within the bone marrow (BM) in a complex microenvironmental niche consisting of osteoblasts, stromal cells, adipose tissue, and vascular structures, all implicated in the control of self-renewal and differentiation1,2. As intact BM has been traditionally inaccessible to direct observations, the interactions between HSPC and their microenvironment remains largely uncharacterized in vivo. Previously, we established a methodology to visualize the 3D architecture of intact BM using confocal fluorescence and reflection microscopy3. We characterized expansion of EGFP-marked HSPCs in the BM, but the use of only a single FP precluded analysis of regeneration at a clonal level. Very recently we took advantage of the Lentiviral Gene Ontology (LeGO) vectors constitutively expressing fluorescent proteins (FPs) to efficiently mark cells4,5. Co-transduction of HSPC with 3 or 5 vectors generates a diverse palette of combinatorial colors, allowing tracking of multiple individual HSPC clones.
Marked HSPC combined with new imaging technology permitted to trace individual HSPC homing and engraftment in the BM of irradiated mice. LeGO vectors were used to mark HSPC with 3 or 5 different FPs (from Cerulean, eGFP, Venus, tdTomato, and mCherry) and follow their engraftment over time in the BM by confocal and 2-photon microscopy, allowing clear visualization of bone and other matrix structures, and the relation of HSPC clones to components of their microenvironment. HSPC were purified as the lineage negative cells from C57Bl/6 mice BM, transduced with LeGO vectors, and reinfused by tail vein injection into myelo-ablated congenic mice. By monitoring large volumes of the sternum BM tissue we visualized endosteal engraftment occurring early in BM regeneration. Cell clusters with diverse color spectra appeared initially in close proximity to the bone and progressed centrally over time. Interestingly, after more than 3 weeks the marrow consisted of macroscopic clonal clusters, suggesting spread of hematopoiesis derived from individual HSPCs contiguously in the marrow, rather than widespread dissemination of HSPCs via the bloodstream. There was less color diversity at late time points, suggesting difficulty in transducing long-term repopulating cells with multiple vectors.
In addition, HSPCs formed clusters in the spleen, an organ also responsible for hematopoiesis in mice. HPSC-derived individual cells could be resolved in the thymus, lymph nodes, spleen, liver, lung, heart, skin, skeletal muscle, adipose tissue, and kidney as well. The 3D images can be assessed qualitatively and quantitatively to appreciate the distribution of cells with minimal perturbations of the tissues. Finally, we illustrated the feasibility of live dynamic studies in 4D by combining resonant scanning multiphoton and confocal time-lapse imaging. This methodology enables non-invasive high resolution, multidimensional cell-fate tracing of spectrally marked cells populations in their intact 3D architecture, providing a powerful tool in the study of tissue regeneration and pathology.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Production of viruses</td>
			<td style="width:493px;"></td>
			<td style="width:216px;"></td>
			<td style="width:343px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">LeGO-Cer2</td>
			<td style="width:493px;">Addgene</td>
			<td style="width:216px;">27338</td>
			<td>Expression of Cerulean</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">LeGO-G2</td>
			<td style="width:493px;">Addgene</td>
			<td style="width:216px;">25917</td>
			<td>Expression of eGFP</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">LeGO-V2</td>
			<td style="width:493px;">Addgene</td>
			<td style="width:216px;">27340</td>
			<td>Expression of Venus</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">LeGO-T2</td>
			<td style="width:493px;">Addgene</td>
			<td style="width:216px;">27342</td>
			<td>Expression of tdTomato</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">LeGO-C2</td>
			<td style="width:493px;">Addgene</td>
			<td style="width:216px;">27339</td>
			<td>Expression of mCherry</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Calciumm Phosphate Transfection Kit</td>
			<td>Sigma</td>
			<td>CAPHOS-1KT</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Tissue culture dish</td>
			<td style="width:493px;">BD Falcon</td>
			<td style="width:216px;">353003</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">IMDM</td>
			<td style="width:493px;">Gibco, Life Technology</td>
			<td style="width:216px;">12440-053</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Fetal Bovine Serum Heat Inactivated</td>
			<td style="width:493px;">Sigma</td>
			<td style="width:216px;">F4135-500ML</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Pen Strep Glutamine</td>
			<td style="width:493px;">Gibco, Life Technology</td>
			<td style="width:216px;">10378-016</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Centrifuge Tubes</td>
			<td style="width:493px;">Beckman Coulter</td>
			<td style="width:216px;">326823</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">SW28 Ultracentrifuge</td>
			<td style="width:493px;">Beckman Coulter</td>
			<td style="width:216px;">L60</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Millex Syringe Driven Filter Unite (0.22um)</td>
			<td style="width:493px;">Millipore</td>
			<td style="width:216px;">SLGS033SS</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;"></td>
			<td style="width:493px;"></td>
			<td style="width:216px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Mouse cell collection, purification, transduction and transplantation</td>
			<td style="width:493px;"></td>
			<td style="width:216px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">ACK lysing buffer</td>
			<td style="width:493px;">Quality Biologicals Inc.</td>
			<td style="width:216px;">118-156-101</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Lineage Cell Depletion Kit (mouse)</td>
			<td>Miltenyi Biotec Inc. USA</td>
			<td>130-090-858</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">LS columns + tubes</td>
			<td>Miltenyi Biotec Inc. USA</td>
			<td>130-041-306</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Pre-Separation Filters (30um)</td>
			<td>Miltenyi Biotec Inc. USA</td>
			<td>130-041-407</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:493px;">StemSpan SFEM serum-free medium for culture and expansion of hematopoietic cells (500mL)</td>
			<td>StemCell Technologies Inc&#160;</td>
			<td>9650</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">murine IL-11 CF</td>
			<td>R &#38; D Systems Inc</td>
			<td>418-ML-025/CF</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">recombinant murine SCF</td>
			<td style="width:493px;">RDI Division of Fitzgerald Industries Intl&#160;</td>
			<td>RDI-2503</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">recombinant murine IL-3</td>
			<td>R &#38; D Systems Inc</td>
			<td>403-ML-050</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">FLT-3 Ligand</td>
			<td>Miltenyi Biotec Inc. USA</td>
			<td>130-096-480</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">12-well plates, Costar</td>
			<td style="width:493px;">Corning Inc.</td>
			<td style="width:216px;">3527</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Retronectin</td>
			<td style="width:493px;">Takara Bio Inc</td>
			<td style="width:216px;">T100A/B</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Protamine Sulfate</td>
			<td style="width:493px;">Sigma</td>
			<td style="width:216px;">P-4020</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;"></td>
			<td style="width:493px;"></td>
			<td style="width:216px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Confocal and two-photon microscopy</td>
			<td style="width:493px;"></td>
			<td style="width:216px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">DMEM</td>
			<td style="width:493px;">Lonza</td>
			<td style="width:216px;">12-614F</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">1M Hepes</td>
			<td style="width:493px;">Cellgro, Mediatech Inc.</td>
			<td style="width:216px;">25-060-CI</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Glass bottom culture dish P35G-0-20-C</td>
			<td>MatTek Corporation</td>
			<td>P35G-0-20-C</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Glass bottom culture dish P35G-0-14-C</td>
			<td>MatTek Corporation</td>
			<td>P35G-0-14-C</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Nunc Lab-Tek Chambered Coverglass #1 Borosilicate coverglass; 4-well</td>
			<td>Thermo Scientific</td>
			<td>155383</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;"></td>
			<td style="width:493px;"></td>
			<td style="width:216px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Leica TCS SP5 AOBS five channels confocal and multi-photon microscope</td>
			<td style="width:493px;">Leica Microsystems</td>
			<td style="width:216px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Chameleon Vision II -TiSaph laser range 680-1080nm</td>
			<td style="width:493px;">Coherent</td>
			<td style="width:216px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Chameleon Compact OPO laser range 1030-1350nm</td>
			<td style="width:493px;">Coherent</td>
			<td style="width:216px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HCX-IRAPO-L 25x/0.95 NA water dipping objective (WD=2.5 mm)</td>
			<td style="width:493px;">Leica Microsystems</td>
			<td style="width:216px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HC-PLAPO-CS 20x/0.70 NA dry objective (WD=0.6 mm)</td>
			<td style="width:493px;">Leica Microsystems</td>
			<td style="width:216px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HC-PL-IRAPO 40x/1.1NA water immersion objective (WD=0.6 mm)</td>
			<td style="width:493px;">Leica Microsystems</td>
			<td style="width:216px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;"></td>
			<td style="width:493px;"></td>
			<td style="width:216px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:493px;">Imaris software version 7.6</td>
			<td style="width:493px;">Bitplane</td>
			<td style="width:216px;"></td>
			<td></td>
		</tr>
	</tbody>
</table>

in vivo clonal tracking of hematopoietic stem and progenitor cells marked by five fluorescent proteins using confocal and multiphoton microscopy

We developed and validated a fluorescent marking methodology for clonal tracking of hematopoietic stem and progenitor cells (HSPCs) with high spatial and temporal resolution to study in vivo hematopoiesis using the murine bone marrow transplant experimental model. Genetic combinatorial marking using lentiviral vectors encoding fluorescent proteins (FPs) enabled cell fate mapping through advanced microscopy imaging. Vectors encoding five different FPs: Cerulean, EGFP, Venus, tdTomato, and mCherry were used to concurrently transduce HSPCs, creating a diverse palette of color marked cells. Imaging using confocal/two-photon hybrid microscopy enables simultaneous high resolution assessment of uniquely marked cells and their progeny in conjunction with structural components of the tissues. Volumetric analyses over large areas reveal that spectrally coded HSPC-derived cells can be detected non-invasively in various intact tissues, including the bone marrow (BM), for extensive periods of time following transplantation. Live studies combining video-rate multiphoton and confocal time-lapse imaging in 4D demonstrate the possibility of dynamic cellular and clonal tracking in a quantitative manner.

Whole-mount 3D confocal/2-photon microscopy reconstructions of the sternal bone marrow time course revealed the engraftment and expansion of transplanted co-5FPs in a pattern with remarkable characteristics: clones appeared clearly delineated, homogenously marked with wide palette of colors initially and progress over time to preferentially contain cells of mostly one color. Confocal microscopy setup and representative examples of imaging 5FPs-marked HSPC in the sternal bone marrow are illustrated in Figure 2</st...

Watch this Scientific Journal Video about In vivo Clonal Tracking of Hematopoietic Stem and Progenitor Cells Marked by Five Fluorescent Proteins using Confocal and Multiphoton Microscopy at JoVE.com

In vivo Clonal Tracking of Hematopoietic Stem and Progenitor Cells Marked by Five Fluorescent Proteins using Confocal and Multiphoton Microscopy

Combinatorial 5 fluorescent proteins marking of hematopoietic stem and progenitor cells allows in vivo clonal tracking via confocal and two-photon microscopy, providing insights into bone marrow hematopoietic architecture during regeneration. This method allows non-invasive fate mapping of spectrally-coded HSPCs-derived cells in intact tissues for extensive periods of time following transplantation.

In vivo Clonal Tracking of Hematopoietic Stem and Progenitor Cells Marked by Five Fluorescent Proteins using Confocal and Multiphoton Microscopy

We developed and validated a fluorescent marking methodology for clonal tracking of hematopoietic stem and progenitor cells (HSPCs) with high spatial and ...

in-vivo-clonal-tracking-hematopoietic-stem-progenitor-cells-marked

Research

JoVE Journal

Biology

13.1K Views.  NHLBI/NIH. Combinatorial 5 fluorescent proteins marking of hematopoietic stem and progenitor cells allows in vivo clonal tracking via confocal and two-photon microscopy, providing insights into bone marrow hematopoietic architecture during regeneration. This method allows non-invasive fate mapping of spectrally-coded HSPCs-derived cells in intact tissues for extensive periods of time following transplantation. 

Video: In vivo Clonal Tracking of Hematopoietic Stem and Progenitor Cells Marked by Five Fluorescent Proteins using Confocal and Multiphoton Microscopy

Isolation and Transplantation of Hematopoietic Stem Cells (HSCs)

Isolation and Transplantation of Hematopoietic Stem Cells HSCs

Tracking Dynamics of Muscle Engraftment in Small Animals by In Vivo Fluorescent Imaging

Muscular dystrophies are a group of degenerative muscle diseases characterized by progressive loss of contractile muscle cells. Currently, there is no curative treatment available. Recent advances in stem cell biology have generated new hopes for the development of effective cell based therapies to treat these diseases. Transplantation of various types of stem cells labeled with fluorescent proteins into muscles of dystrophic animal models has been used broadly in the field. A non-invasive technique with the capability to track the transplanted cell fate longitudinally can further our ability to evaluate muscle engraftment by transplanted cells more accurately and efficiently.
In the present study, we demonstrate that in vivo fluorescence imaging is a sensitive and reliable method for tracking transplanted GFP (Green Fluorescent Protein)-labeled cells in mouse skeletal muscles. Despite the concern about background due to the use of an external light necessary for excitation of fluorescent protein, we found that by using either nude mouse or eliminating hair with hair removal reagents much of this problem is eliminated. Using a CCD camera, the fluorescent signal can be detected in the tibialis anterior (TA) muscle after injection of 5 x 105 cells from either GFP transgenic mice or eGFP transduced myoblast culture. For more superficial muscles such as the extensor digitorum longus (EDL), injection of fewer cells produces a detectable signal. Signal intensity can be measured and quantified as the number of emitted photons per second in a region of interest (ROI). Since the acquired images show clear boundaries demarcating the engrafted area, the size of the ROI can be measured as well. If the legs are positioned consistently every time, the changes in total number of photons per second per muscle and the size of the ROI reflect the changes in the number of engrafted cells and the size of the engrafted area. Therefore the changes in the same muscle over time are quantifiable. In vivo fluorescent imaging technique has been used primarily to track the growth of tumorogenic cells, our study shows that it is a powerful tool that enables us to track the fate of transplanted stem cells.

Tracking Dynamics of Muscle Engraftment in Small Animals by In Vivo Fluorescent Imaging

We describe an in vivo fluorescence imaging protocol to monitor muscle regeneration by GFP-labeled myoblasts after transplantation into skeletal muscles of both healthy and dystrophic mice. This protocol can be adapted to study muscle regeneration by transplantation of other types of cells and in other muscular conditions as well.

Muscular dystrophies are a group of degenerative muscle diseases characterized by progressive loss of contractile muscle cells. Currently, there is no ...

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

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

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

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

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

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 ...

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) ...

A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions

Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex signaling mechanisms underlying filopodial initiation, elongation and subsequent stabilization or retraction, it is crucial to determine the spatio-temporal protein activity in these dynamic structures. To analyze protein function in filopodia, we recently developed a semi-automated tracking algorithm that adapts to filopodial shape-changes, thus allowing parallel analysis of protrusion dynamics and relative protein concentration along the whole filopodial length. Here, we present a detailed step-by-step protocol for optimized cell handling, image acquisition and software analysis. We further provide instructions for the use of optional features during image analysis and data representation, as well as troubleshooting guidelines for all critical steps along the way. Finally, we also include a comparison of the described image analysis software with other programs available for filopodia quantification. Together, the presented protocol provides a framework for accurate analysis of protein dynamics in filopodial protrusions using image analysis software.

We present a software solution for semi-automated tracking of relative protein concentration along the length of dynamic cellular protrusions.

Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex ...

Visualizing Lymph Node Structure and Cellular Localization using Ex-Vivo Confocal Microscopy

Lymph nodes (LNs) are organs spread within the body, where the innate immune responses can connect with the adaptive immunity. In fact, LNs are strategically interposed in the path of the lymphatic vessels, allowing intimate contact of tissue antigens with all resident immune cells in the LN. Thus, understanding the cellular composition, distribution, location and interaction using ex vivo whole LN imaging will add to the knowledge on how the body coordinates local and systemic immune responses. This protocol shows an ex vivo imaging strategy following an in vivo administration of fluorescent-labeled antibodies that allows a very reproducible and easy-to-perform methodology by using conventional confocal microscopes and stock reagents. Through subcutaneous injection of antibodies, it is possible to label different cell populations in draining LNs without affecting tissue structures that can be potentially damaged by a conventional immunofluorescence microscopy technique.

This protocol describes a technique to image different cell populations in draining lymph nodes without alterations in the organ structure.

Lymph nodes (LNs) are organs spread within the body, where the innate immune responses can connect with the adaptive immunity. In fact, LNs are ...

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

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

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

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

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

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

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

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

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

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

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

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