We thank members of our laboratory for their helpful discussions and support. Our research on breast cancer stem cells and the tumor microenvironment is funded by grants from the Canadian Cancer Research Society Research Institute and the U.S. Army Department of Defense Breast Cancer Program (Grant # BC160912). V.B. is supported by a Western Postdoctoral Fellowship (Western University), and both A.L.A. and V.B. are supported by the Breast Cancer Society of Canada. C.L. is supported by a Vanier Canada Graduate Scholarship from the Government of Canada.

Collection of patient-derived surgical or biopsy samples directly from consenting breast cancer patients were carried out under approved human ethics protocol approved by the institutional ethic board. All mice used to generate patient-derived xenograft models were maintained and housed in an institution approved animal facility. The tumor tissue from patient-derived xenograft models using mice were generated as per approved ethics protocol approved by the institutional animal care committee.
1....

Breast cancer metastasis and resistance to therapy have become major cause of mortality in women worldwide. The existence of a sub-population of breast cancer stem cells (BCSCs) contributes to enhanced metastasis26,43,44,45,46 and therapy resistance21,47,48. Therefore...

Understanding the cellular and molecular mechanisms of human breast cancer stem cells (BCSCs) is crucial for addressing the challenges encountered in breast cancer treatment. The emergence of the BCSC concept dates back to the early 21st century, where a small population of CD44+CD24-/low breast cancer cells were found to be capable of generating heterogenous tumors in mice1,2. Subsequently, it was observed that human breast cancer cells with high enzymatic activity of aldehyde dehydrogenase (ALDHhigh) also displayed similar stem cell-like properties3. These BCSCs represent a small population of cells capable of self-renewal and differentiation, contributing to the heterogenous nature of bulk tumors1,2,3. Accumulating evidence suggest that alterations in evolutionarily conserved signaling pathways drive BCSC survival and maintenance4,5,6,7,8,9,10,11,12,13,14. In addition, the cell extrinsic microenvironment has been shown to play a pivotal role in dictating different BCSC functions15,16,17. These molecular pathways and the external factors regulating BCSC function contribute to breast cancer relapse, metastasis18 and development of resistance to therapies19,20,21, with the residual existence of BCSCs post-treatment posing a major challenge to the overall survival of breast cancer patients22,23. Pre-clinical evaluation of these factors is therefore very important for identifying BCSC-targeting therapies that could be beneficial for achieving better treatment outcomes and improved overall survival in breast cancer patients.
Several in vitro human breast cancer cell line models and in vivo human xenograft models have been used to characterize BCSCs24,25,26,27,28,29. The ability of cell lines to continuously repopulate after every successive passage makes these an ideal model system to perform omics-based and pharmacogenomic studies. However, cell lines often fail to recapitulate the heterogeneity observed in patient samples. Hence, it is important to complement cell line data with patient-derived samples. Isolation of BCSCs in their purest form is important for enabling detailed characterization of BCSCs. Achieving this purity depends on the selection of phenotypic markers that are specific to BCSCs. Currently, the ALDHhighCD44+CD24- cell phenotype is most commonly used to distinguish and isolate human BCSCs from bulk breast cancer cell populations using fluorescence activated cell sorting (FACS) for maximum purity1,3,26. Furthermore, the properties of isolated BCSCs such as self-renewal, proliferation, and differentiation can be evaluated using in vitro and in vivo techniques.
For example, in vitro colony forming assays can be used to assess the ability of a single cell to self-renew to form a colony of 50 cells or more in presence of different treatment conditions30. Mammosphere assays can also be used to assess the self-renewal potential of breast cancer cells under anchorage-independent conditions. This assay measures the ability of single cells to generate and grow as spheres (mixture of BCSCs and non-BCSCs) at each successive passage in serum-free non-adherent culture conditions31. Additionally, 3-Dimensional (3D) culture models can be used to assess BCSC function, including cell-cell and cell-matrix interactions that closely recapitulate the in vivo microenvironment and allow investigation of the activity of potential BCSC-targeted therapies32. Despite the diverse applications of in vitro models, it is difficult to model the complexity of in vivo conditions using only in vitro assays. This challenge can be overcome by use of mouse xenograft models to evaluate BCSC behavior in vivo. In particular, such models serve as an ideal system for assessing breast cancer metastasis33, investigating interactions with the microenvironment during disease progression34, in vivo imaging35, and for predicting patient-specific toxicity and efficacy of antitumor agents34.
This protocol provides a detailed description for the isolation of human ALDHhighCD44+CD24- BCSCs at maximum purity from bulk populations of heterogenous breast cancer cells. We also provide a detailed description of three in vitro techniques (colony forming assay, mammosphere assay, and 3D culture model) and an in vivo tumor xenograft assay that can be used to assess different functions of BCSCs. These methods would be appropriate for use by investigators interested in isolating and characterizing BCSCs from human breast cancer cell lines or primary-patient derived breast cancer cells and tumor tissue for the purposes of understanding BCSC biology and/or investigating novel BCSC-targeting therapies.

<table>
	<tbody>
		<tr>
			<td>7-Aminoactinomycin D (7AAD)</td>
			<td>BD</td>
			<td>51-68981E</td>
			<td>suggested: 0.25 &#181;g/1x106 cells</td>
		</tr>
		<tr>
			<td>Acetone</td>
			<td>Fisher</td>
			<td>A18-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Aldehyde dehydrogenase (ALDH) substrate</td>
			<td>Stemcell Technologies</td>
			<td>1700</td>
			<td>Sold commerically as part of the ALDEFLOUR Assay kit; follow manufacturer&#39;s instructions for ALDH substrate preparation</td>
		</tr>
		<tr>
			<td>Basement membrane extract (BME)</td>
			<td>Corning</td>
			<td>354234</td>
			<td>Sold under the commercial name Matrigel</td>
		</tr>
		<tr>
			<td>Cell culture plates: 6 well</td>
			<td>Corning</td>
			<td>877218</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell culture plates: 60mm</td>
			<td>Corning</td>
			<td>353002</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell culture plates: 96-well ultra low attachment</td>
			<td>Corning</td>
			<td>3474</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell strainer: 40 micron</td>
			<td>BD</td>
			<td>352340</td>
			<td></td>
		</tr>
		<tr>
			<td>Collagen</td>
			<td>Stemcell Technologies</td>
			<td>7001</td>
			<td>Prepare 1:30 dilution of 3 mg/mL collagen in PBS</td>
		</tr>
		<tr>
			<td>Collagenase</td>
			<td>Sigma</td>
			<td>11088807001</td>
			<td>1x</td>
		</tr>
		<tr>
			<td>Conical tubes: 50 mL</td>
			<td>Fisher scientific</td>
			<td>05-539-7</td>
			<td></td>
		</tr>
		<tr>
			<td>Crystal violet</td>
			<td>Sigma</td>
			<td>C6158</td>
			<td>Use 0.05% crystal violet solution in water for staining</td>
		</tr>
		<tr>
			<td>Dispase</td>
			<td>Stemcell Technologies</td>
			<td>7913</td>
			<td>5U/mL</td>
		</tr>
		<tr>
			<td>DMEM:F12</td>
			<td>Gibco</td>
			<td>11330-032</td>
			<td>1x, With L-glutamine and 15 mM HEPES</td>
		</tr>
		<tr>
			<td>DNAse</td>
			<td>Sigma</td>
			<td>D5052</td>
			<td>0.1 mg/mL final concentration</td>
		</tr>
		<tr>
			<td>FBS</td>
			<td>Avantor Seradigm Lifescience</td>
			<td>97068-085</td>
			<td>&#160;</td>
		</tr>
		<tr>
			<td>Flow tubes: 5ml</td>
			<td>BD</td>
			<td>352063</td>
			<td>Polypropylene round-bottom tubes</td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Fisher</td>
			<td>84124</td>
			<td></td>
		</tr>
		<tr>
			<td>mouse anti-Human CD24 antibody</td>
			<td>BD</td>
			<td>561646</td>
			<td>R-phycoerythrin and Cyanine dye conjugated Clone: ML5</td>
		</tr>
		<tr>
			<td>mouse anti-Human CD44 antibody</td>
			<td>BD</td>
			<td>555479</td>
			<td>R-phycoerythrin conjugated, Clone: G44-26</td>
		</tr>
		<tr>
			<td>N,N-diethylaminobenzaldehyde (DEAB)</td>
			<td>Stemcell Technologies</td>
			<td>1700</td>
			<td>Sold commerically as part of the ALDEFLOUR Assay kit; follow manufacturer&#39;s instructions DEAB preparation</td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Wisent Inc</td>
			<td>311-425-CL</td>
			<td>1x, Without calcium and magnesium</td>
		</tr>
		<tr>
			<td>Trypsin-EDTA</td>
			<td>Gibco</td>
			<td>25200-056</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Mammosphere Media Composition</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>B27</td>
			<td>Gibco</td>
			<td>17504-44</td>
			<td>1x</td>
		</tr>
		<tr>
			<td>bFGF</td>
			<td>Sigma</td>
			<td>F2006</td>
			<td>10 ng/mL</td>
		</tr>
		<tr>
			<td>BSA</td>
			<td>Bioshop</td>
			<td>ALB003</td>
			<td>04%</td>
		</tr>
		<tr>
			<td>DMEM:F12</td>
			<td>Gibco</td>
			<td>11330-032</td>
			<td>1x, With L-glutamine and 15 mM HEPES</td>
		</tr>
		<tr>
			<td>EGF</td>
			<td>Sigma</td>
			<td>E9644</td>
			<td>20 ng/mL</td>
		</tr>
		<tr>
			<td>Insulin</td>
			<td>Sigma</td>
			<td>16634</td>
			<td>5 &#181;g/mL</td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>3D Organoid Media Composition</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>A8301</td>
			<td>Tocris</td>
			<td>2939</td>
			<td>500 nM</td>
		</tr>
		<tr>
			<td>B27</td>
			<td>Gibco</td>
			<td>17504-44</td>
			<td>1x</td>
		</tr>
		<tr>
			<td>DMEM:F12</td>
			<td>Gibco</td>
			<td>11330-032</td>
			<td>1x, With L-glutamine and 15 mM HEPES</td>
		</tr>
		<tr>
			<td>EGF</td>
			<td>Sigma</td>
			<td>E9644</td>
			<td>5 ng/mL</td>
		</tr>
		<tr>
			<td>FGF10</td>
			<td>Peprotech</td>
			<td>100-26</td>
			<td>20 ng/mL</td>
		</tr>
		<tr>
			<td>FGF7</td>
			<td>Peprotech</td>
			<td>100-19</td>
			<td>5 ng/mL</td>
		</tr>
		<tr>
			<td>GlutaMax</td>
			<td>Invitrogen</td>
			<td>35050-061</td>
			<td>1x</td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Gibco</td>
			<td>15630-080</td>
			<td>10 mM</td>
		</tr>
		<tr>
			<td>N-acetylcysteine</td>
			<td>Sigma</td>
			<td>A9165</td>
			<td>1.25 mM</td>
		</tr>
		<tr>
			<td>Neuregulin &#946;1</td>
			<td>Peprotech</td>
			<td>100-03</td>
			<td>5 nM</td>
		</tr>
		<tr>
			<td>Nicotinamide</td>
			<td>Sigma</td>
			<td>N0636</td>
			<td>5 mM</td>
		</tr>
		<tr>
			<td>Noggin</td>
			<td>Peprotech</td>
			<td>120-10C</td>
			<td>100 ng/mL</td>
		</tr>
		<tr>
			<td>R-spondin3</td>
			<td>R&#38;D</td>
			<td>3500</td>
			<td>250 ng/mL</td>
		</tr>
		<tr>
			<td>SB202190</td>
			<td>Sigma</td>
			<td>S7067</td>
			<td>500 nM</td>
		</tr>
		<tr>
			<td>Y-27632</td>
			<td>Tocris</td>
			<td>1254</td>
			<td>5 &#181;M</td>
		</tr>
	</tbody>
</table>

isolation and functional assessment of human breast cancer stem cells from cell and tissue samples

Breast cancer stem cells (BCSCs) are cancer cells with inherited or acquired stem cell-like characteristics. Despite their low frequency, they are major contributors to breast cancer initiation, relapse, metastasis and therapy resistance. It is imperative to understand the biology of breast cancer stem cells in order to identify novel therapeutic targets to treat breast cancer. Breast cancer stem cells are isolated and characterized based on expression of unique cell surface markers such as CD44, CD24 and enzymatic activity of aldehyde dehydrogenase (ALDH). These ALDHhighCD44+CD24- cells constitute the BCSC population and can be isolated by fluorescence-activated cell sorting (FACS) for downstream functional studies. Depending on the scientific question, different in vitro and in vivo methods can be used to assess the functional characteristics of BCSCs. Here, we provide a detailed experimental protocol for isolation of human BCSCs from both heterogenous populations of breast cancer cells as well as primary tumor tissue obtained from breast cancer patients. In addition, we highlight downstream in vitro and in vivo functional assays including colony forming assays, mammosphere assays, 3D culture models and tumor xenograft assays that can be used to assess BCSC function.

The described protocol allows isolation of human BCSCs from a heterogenous population of breast cancer cells, either from cell lines or from dissociated tumor tissue. For any given cell line or tissue sample, it is crucial to generate a uniform single cell suspension to isolate BCSCs at maximum purity as contaminating non-BCSC populations could result in variable cellular responses, especially if the study aim is to evaluate the efficacy of therapeutic agents targeting BCSCs. Application of a stringent sorting strategy w...

Watch this Scientific Journal Video about Isolation and Functional Assessment of Human Breast Cancer Stem Cells from Cell and Tissue Samples at JoVE.com

Isolation and Functional Assessment of Human Breast Cancer Stem Cells from Cell and Tissue Samples

This experimental protocol describes the isolation of BCSCs from breast cancer cell and tissue samples as well as the in vitro and in vivo assays that can be used to assess BCSC phenotype and function.

Breast cancer stem cells (BCSCs) are cancer cells with inherited or acquired stem cell-like characteristics. Despite their low frequency, they are major ...

This technique will allow researchers to isolate breast cancer stem cells at maximum purity and viability for the performance of both in vitro and in vivo functional characterization assays. Isolated breast cancer stem cells can also be used to help elucidate the molecular events that control tumorigenicity and metastasis, and to design therapeutic strategies to target these cells. With minor modifications specific to the cell and tissue types of interest, this method can also be applied to other systems.To generate a single cell suspension from a cell culture, wash an 80%confluent breast cancer cell culture with PBS and treat the cells with an appropriate cell dissociation solution for five minutes at room temperature. Once the cells have detached, add five milliliters of culture medium to neutralize the cell dissociation solution and transfer the cells to a 50 milliliter conical tube for centrifugation. Resuspend the pellet in five milliliters of PBS for counting.After counting, centrifuge the cells again, then resuspend the cells at one times 10 to six cells per milliliter of ALDH substrate buffer. To generate a single cell suspension from a tissue sample, use surgical blades in a crisscross technique to mince the tumor tissue into approximately one millimeter size pieces. Place the pieces in a 50 milliliter conical tube containing 10 milliliters of dissociation buffer.Seal the tube with parafilm for a 40 minute incubation at 37 degrees Celsius in a shaker and sediment the digested tissue pieces by centrifugation. Resuspend the pellet in five milliliters of trypsin using a five milliliter pipette and incubate the tissue in a 37 degree water bath for five minutes. At the end of the incubation, vigorously pipette the tissue several times to release single cells and add enough DMEM/F-12 medium to bring the total volume in the tube to 25 milliliters.Collect the cells by centrifugation, resuspend the pellet in one milliliter of Displace DNAse, and incubate for five minutes in a 37 degree Celsius water bath. At the end of the incubation, bring the total volume to 10 milliliters with PBS. Mix the cells by pipetting and passage them through a 40 micron cell strainer into a 50 milliliter tube.After centrifugation, resuspend the cells in five milliliters of fresh PBS for counting. To perform a colony forming assay, after sorting, resuspend the cells in complete medium and add the appropriate number of breast cancer stem cells to each of the three tubes containing two milliliters of medium per tube, labeled one times 10 to the second, two times 10 to the second, or five times 10 to the second cells. Pipette up and down five times to thoroughly mix the cell suspension and plate the cells into individual wells of a six well plate.Gently swirl the plate to obtain uniform cell distributions and place the plate in the cell culture incubator until colonies appear. At the end of the incubation, wash the cells with one milliliter of PBS per well and stain the cells with 500 microliters of 0.05%crystal violet solution per well for 30 seconds. At the end of the incubation, wash the wells two times with two milliliters of water per well to remove the excess dye, and count and record the total number of colonies per well by light microscopy at a four or 10 times magnification.To perform a mammosphere assay, after sorting, resuspend the cells in complete mammosphere medium and plate the at a seating density of five times 10 of the second cells per square centimeter area per well in a 96 well ultra-low attachment cell culture plate. Before counting the number of mammospheres per well by light microscopy, place the plate in the cell culture incubator for five to 10 days. To set up a 3D culture model, carefully add 50 microliters of basement membrane extract to each well of a 96 well plate without bubbles and place the plate at 37 degrees Celsius for one hour to allow the solution to polymerize.Add 100 microliters of PBS after 10 minutes to avoid drying of the gel layer. At the end of the incubation, suspend the sorted cells to five to 50 times 10 to the third cells per 200 microliters of 3D culture medium concentration and replace the PBS in each well of the 96 well plate with 200 microliters of media containing cells. Then place the plate in the cell culture incubator for 10 to 14 days before assessing the cultures for organoid formation.Human breast cancer cells that exhibit enhanced ALDH enzymatic activity express high levels of CD44 and low to negative levels of expression of CD24, and can be classified as breast cancer stem cells. The proportion of breast cancer stem cells within the bulk population can vary between cell lines or patients and often depends on the disease stage, with more aggressive breast cancer typically displaying a higher proportion of breast cancer stem cells. The ability of a single breast cancer cell to self-renew and generate colonies of 50 cells can be assessed by colony forming assays.The ability of breast cancer stem cells to self-renew under anchorage-independent experimental conditions can be assessed by mammosphere assays. Culturing breast cancer cells and basement membrane extract allows breast cancer stem cells to form 3D structures that recapitulate in vivo conditions. In addition, in vivo mouse xenograft models can be used to understand the differences in growth, self-renewal, differentiation, and/or the tumor initiating ability of breast cancer stem cells compared to non-breast cancer stem cells or bulk cell populations.Following this procedure, the isolated breast cancer stem cells can be used in transcriptomic, kinomic, and metabolomic studies. This method provides researchers with an opportunity to explore the role of breast cancer stem cells in tumor initiation, metastasis, recurrence, and therapy resistance.

Isolation and Functional Assessment of Human Breast Cancer Stem Cells from Cell and Tissue Samples

Abstract