Funding for this research was provided by the National Cancer Institute (R37CA227656 to JSB). This research was also supported by the Flow Cytometry and Immune Monitoring Shared Resources of the University of Kentucky Markey Cancer Center (P30CA177558).

In this protocol, we are using GFP-labeled zebrafish T-ALL cells that were generated previously in the CG1 strain and thus can be directly injected into recipient syngeneic CG1 zebrafish15. Briefly, leukemia was generated by DNA microinjection of rag2:Myc and rag2:GFP into single-cell CG1 zebrafish embryos. Animals were monitored for leukemia development starting at 3 weeks post injection, using fluorescence microscopy. GFP-positive leukemia cells were FACS isolated and serially ...

Estimating LSC Frequency in Zebrafish T-ALL Using Cell Proliferation Dye Sorting

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	<li>Reya, T., Morrison, S. J., Clarke, M. F., Weissman, I. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stem+cells,+cancer,+and+cancer+stem+cells.">Stem cells, cancer, and cancer stem cells.</a> Nature. 414 (6859), 105-111 (2001).</li><li>Arai, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tie2/angiopoietin-1+signaling+regulates+hematopoietic+stem+cell+quiescence+in+the+bone+marrow+niche.">Tie2/angiopoietin-1 signaling regulates hematopoietic stem cell quiescence in the bone marrow niche.</a> Cell. 118 (2), 149-161 (2004).</li><li>Li, L., Bhatia, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stem+cell+quiescence.">Stem cell quiescence.</a> Clin. 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B. <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+produced+by+altered+tumor+metabolism+impacts+cancer+stem+cell+maintenance.">Reactive oxygen species produced by altered tumor metabolism impacts cancer stem cell maintenance.</a> Redox Biol. 44, 101953 (2021).</li><li>Zhou, B. -. B. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tumour-initiating+cells:+Challenges+and+opportunities+for+anticancer+drug+discovery.">Tumour-initiating cells: Challenges and opportunities for anticancer drug discovery.</a> Nat Rev Drug Discov. 8 (10), 806-823 (2009).</li><li>Lyons, A. B., Blake, S. J., Doherty, K. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Flow+cytometric+analysis+of+cell+division+by+dilution+of+cfse+and+related+dyes.">Flow cytometric analysis of cell division by dilution of cfse and related dyes.</a> Curr Protoc Cytom. 64 (1), 9.11.11-19.11.12 (2013).</li><li>Lyons, A. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysing+cell+division+in+vivo+and+in+vitro+using+flow+cytometric+measurement+of+cfse+dye+dilution.">Analysing cell division in vivo and in vitro using flow cytometric measurement of cfse dye dilution.</a> J Immunol Methods. 243 (1-2), 147-154 (2000).</li><li>Azari, H., Deleyrolle, L. P., Reynolds, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Using+carboxy+fluorescein+succinimidyl+ester+(cfse)+to+identify+quiescent+glioblastoma+stem-like+cells.">Using carboxy fluorescein succinimidyl ester (cfse) to identify quiescent glioblastoma stem-like cells.</a> Methods Mol Biol. 1686, 59-67 (2018).</li><li>Deleyrolle, L. P., Rohaus, M. R., Fortin, J. M., Reynolds, B. A., Azari, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+and+isolation+of+slow-dividing+cells+in+human+glioblastoma+using+carboxy+fluorescein+succinimidyl+ester+(cfse).">Identification and isolation of slow-dividing cells in human glioblastoma using carboxy fluorescein succinimidyl ester (cfse).</a> J Vis Exp. (62), e3918 (2012).</li><li>Ebinger, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+rare,+dormant,+and+therapy-resistant+cells+in+acute+lymphoblastic+leukemia.">Characterization of rare, dormant, and therapy-resistant cells in acute lymphoblastic leukemia.</a> Cancer Cell. 30 (6), 849-862 (2016).</li><li>Langenau, D. 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=Myc-induced+t+cell+leukemia+in+transgenic+zebrafish.">Myc-induced t cell leukemia in transgenic zebrafish.</a> Science. 299 (5608), 887-890 (2003).</li><li>Blackburn, J. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clonal+evolution+enhances+leukemia-propagating+cell+frequency+in+t+cell+acute+lymphoblastic+leukemia+through+akt/mtorc1+pathway+activation.">Clonal evolution enhances leukemia-propagating cell frequency in t cell acute lymphoblastic leukemia through akt/mtorc1 pathway activation.</a> Cancer Cell. 25 (3), 366-378 (2014).</li><li>Al-Hamaly, M. A., Turner, L. T., Rivera-Martinez, A., Rodriguez, A., Blackburn, J. 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(53), e2790 (2011).</li><li>Borga, 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=Simultaneous+b+and+t+cell+acute+lymphoblastic+leukemias+in+zebrafish+driven+by+transgenic+myc:+Implications+for+oncogenesis+and+lymphopoiesis.">Simultaneous b and t cell acute lymphoblastic leukemias in zebrafish driven by transgenic myc: Implications for oncogenesis and lymphopoiesis.</a> Leukemia. 33 (2), 333-347 (2019).</li><li>Hu, Y., Smyth, G. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Elda:+Extreme+limiting+dilution+analysis+for+comparing+depleted+and+enriched+populations+in+stem+cell+and+other+assays.">Elda: Extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays.</a> J Immunol Methods. 347 (1-2), 70-78 (2009).</li><li>Bhojwani, D., Pui, C. -. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Relapsed+childhood+acute+lymphoblastic+leukaemia.">Relapsed childhood acute lymphoblastic leukaemia.</a> Lancet Oncol. 14 (6), e205-e217 (2013).</li><li>Zon, L. I., Peterson, R. 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+drug+discovery+in+the+zebrafish.">In vivo drug discovery in the zebrafish.</a> Nat Rev Drug Discov. 4 (1), 35-44 (2005).</li><li>Al-Hamaly, M. 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LSCs are known to be resistant to conventional, anti-proliferative chemotherapy treatments, and finding targeted therapies against these cells holds great promise in reducing the occurrence of relapse and improving patient prognosis20. Previous research described the use of fluorescent cell proliferation stains to identify a small population of quiescent cells associated with drug resistance and stemness in T-ALL PDX models13. In this work, we describe the use of a similar ...

Adult stem cells are responsible for the regeneration of differentiated cell types in a given organ and are predominantly present in a dormant, non-dividing state1,2. For example, hematopoietic stem cells (HSCs), which maintain the blood, largely remain quiescent, and only a small fraction enters the cell cycle to self-renew or differentiate to generate mature blood components3. Similarly, in cancers, a rare subpopulation of cells called cancer stem cells (CSCs) possess the self-renewal ability and are responsible for the long-term maintenance of the malignancy4. Cancer stem cells exist in vivo in a state of quiescence or slow growth, which may enable them to escape the anti-proliferative cancer treatments5, evade clearance by the immune system6, reduce oxidative stress, and enhance their DNA repair pathways7. Even a low number of CSCs left behind after treatment can potentially repopulate the tumor, resulting in a patient&#39;s relapse8. Accordingly, understanding cellular quiescence holds great promise for the identification of potential vulnerabilities of CSCs and the development of new ways to target them.
Cell proliferation dyes, such as the carboxyfluorescein succinimidyl ester (CFSE) stain and its derivatives, are commonly used to track the frequency of cell divisions9. The dye permeates across the cell membrane and, once inside the cell, undergoes activation by intracellular esterases into a fluorescent product. The resultant fluorescent compound is retained inside the cell through the covalent amide bonds formed between the succinimidyl moiety and the amine functional groups of intracellular proteins10. With each cellular division, the fluorescent compound is divided equally between the two resulting cells, causing a two-fold signal dilution. This dye enables the detection of up to 10 cell divisions through flow cytometry analysis11.
This approach has been previously utilized to enrich CSC populations in vitro by identifying slow-cycling populations of cells with high retention of the dye11,12. In T-ALL, CFSE has been used to track tumor growth in vivo in patient-derived xenografts in mice. Following cell labeling and three weeks of transplant, flow cytometry analysis showed a rare population of cells that still retained CFSE fluorescence. This population was associated with stemness, treatment resistance, and high similarity to relapse-causing cells in patients13. Accordingly, this dye provides a useful tool for the study of leukemia stem cell (LSC) phenotypes in T-ALL.
The aim of the work is to extend the application of the cell proliferation dye to study quiescence in vivo using a zebrafish T-ALL model. In particular, the rag2:Myc-driven zebrafish T-ALL model14 provides an excellent venue for the study of self-renewal due to the high frequency of LSCs compared to mouse models and human disease15. In addition, the use of zebrafish allows for large-scale transplantation studies, which can be done at a much lower cost of care and maintenance compared to their mouse counterparts16. Zebrafish are also excellent for live imaging applications, as fluorescently labeled tumor cells can be readily viewed using a simple fluorescence microscope to estimate the rate of tumor development16.
In this protocol, we describe the workflow for staining&#160;zebrafish T-ALL cells with cell proliferation dye followed by&#160;in vivo propagation of stained cells in syngeneic CG1 zebrafish. Upon leukemia development, we describe the sorting of cells that retained the dye and their use for a subsequent limiting dilution transplantation experiment to quantify rates of LSC self-renewal. This protocol can be extended for additional applications, including in vivo drug screening of potential compounds for the targeting of quiescent LSCs. In addition, collected cells can be used for different downstream analyses, such as transcriptomic profiling, proteomics, and metabolomics, offering unique insights into the behavior of quiescent LSCs in T-ALL.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>26 G/2&#8221; micro-syringe</td>
			<td>Hamilton</td>
			<td>87930</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>35 &#181;m filter cap FACS tubes</td>
			<td>Falcon</td>
			<td>352235</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>40 &#181;m cell strainer</td>
			<td>CELLTREAT</td>
			<td>229482</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>96-well skirted PCR plate</td>
			<td>Thermo Fisher Scientific</td>
			<td>AB0800</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>Cell sorter</td>
			<td>Sony Biotechnology</td>
			<td>SY3200</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>CellTrace Far Red</td>
			<td>Thermo Fisher Scientific</td>
			<td>C34564</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>Conical tubes</td>
			<td>VWR</td>
			<td>10026-078</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>Thermo Fisher Scientific</td>
			<td>62248</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>DMSO</td>
			<td>Sigma-Aldrich</td>
			<td>D4818</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>Dulbecco&#39;sPhosphate-buffered saline (PBS)</td>
			<td>Caisson Labs</td>
			<td>22110001</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>Epifluorescence stereo microscope</td>
			<td>Nikon</td>
			<td>SMZ25</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum (FBS)</td>
			<td>Sigma-Aldrich</td>
			<td>12306C</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>Fish system water</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>0.03-0.05% salinity, pH 6.5-8, buffered with sodium bicarbonate</td>
		</tr>
		<tr>
			<td>Microcentrifuge tubes</td>
			<td>Thermo Fisher Scientific</td>
			<td>C2171</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>MS-222</td>
			<td>Pentaire</td>
			<td>TRS-1</td>
			<td>tricaine mesylate, an anesthetic</td>
		</tr>
		<tr>
			<td>Petri dishes</td>
			<td>Corning</td>
			<td>07-202-011</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>Razor blades</td>
			<td>American Line</td>
			<td>66-0089</td>
			<td>NA</td>
		</tr>
		<tr>
			<td>Trypan Blue</td>
			<td>Thermo Fisher Scientific</td>
			<td>T10282</td>
			<td>NA</td>
		</tr>
	</tbody>
</table>

identification of quiescent cells in a zebrafish t-cell acute lymphoblastic leukemia model using cell proliferation staining 

Cellular quiescence is a state of growth arrest or slowed proliferation that is described in normal and cancer stem cells (CSCs). Quiescence may protect CSCs from antiproliferative chemotherapy drugs. In T-cell acute lymphoblastic leukemia (T-ALL) patient-derived xenograft (PDX) mouse models, quiescent cells are associated with treatment resistance and stemness. Cell proliferation dyes are popular tools for the tracking of cell division. The fluorescent dye is covalently anchored into amine groups on the membrane and macromolecules inside the cell. This allows for the tracking of labeled cells for up to 10 divisions, which can be resolved by flow cytometry.
Ultimately, cells with the highest proliferation rates will have low dye retention, as it will be diluted with each cell division, while dormant, slower-dividing cells will have the highest retention. The use of cell proliferation dyes to isolate dormant cells has been optimized and described in T-ALL mouse models. Complementary to the existing mouse models, the rag2:Myc-derived zebrafish T-ALL model provides an excellent venue to interrogate self-renewal in T-ALL due to the high frequency of leukemic stem cells (LSCs) and the convenience of zebrafish for large-scale transplant experiments.
Here, we describe the workflow for the staining of zebrafish T-ALL cells with a cell proliferation dye, optimizing the concentration of the dye for zebrafish cells, passaging successfully stained cells in vivo, and the collection of cells with varying levels of dye retention by live cell sorting from transplanted animals. Given the absence of well-established cell surface makers for LSCs in T-ALL, this approach provides a functional means to interrogate quiescent cells in vivo. For representative results, we describe the engraftment efficiency and the LSC frequency of high and low dye-retaining cells. This method can help investigate additional properties of quiescent cells, including drug response, transcriptional profiles, and morphology.

Author Spotlight: Identification and Isolation of Quiescent Leukemia Stem Cells from Zebrafish T-ALL

Identification of Quiescent Cells in a Zebrafish T-Cell Acute Lymphoblastic Leukemia Model Using Cell Proliferation Staining 

Leukemia stem cells are a rare subpopulation of cells within the leukemia that are responsible for long-term disease maintenance and relapse. Our goal is to better characterize these cells to find ways to target and eliminate them and improve patient outcomes. Cancer stem cells, including leukemia stem cells, exist in a state of quiescence or slow growth, which may enable them to escape anti-proliferative cancer treatments.Understanding cellular quiescence will help identify potential vulnerabilities of leukemia stem cells, and new ways to target them. Using this protocol, we can identify and isolate quiescent leukemia cells from a zebrafish model of T-cell acute lymphoblastic leukemia. Those cells can be used for downstream applications, such as in vivo drug screening, transcriptomic profiling, and proteomics analysis.

We followed the above-described protocol to sort cells that have retained the cell proliferation dye, CT-FR,&#160;and used them for a Limiting dilution assay (LDA) to estimate LSC frequency in the CT-FR High and CT-FR Low populations. To set the gating for the flow cytometry experiment, we used a no fluorophore (no color) control in addition to single-color controls (Figure 2A). Those quadrants were used to identify FITC- and PE-positive and -negative populations for the set...

We used cell proliferation staining to identify quiescent cells in the zebrafish T-acute lymphoblastic leukemia model. The stain is retained in non-dividing cells and reduced during cell proliferation, enabling the selection of dormant cells for further interrogation. This protocol provides a functional tool to study self-renewal in the context of cellular quiescence.

Cellular quiescence is a state of growth arrest or slowed proliferation that is described in normal and cancer stem cells (CSCs). Quiescence may protect ...