This work was supported by the Nature Science Foundation of Guangdong Province (2018A030310586, 2020A1515010989), the Medical Scientific Research Foundation of Guangdong Province (A2019405), the National Natural Science Foundation of China (81772957), the Science and Technology Program of Guangdong Province in China (2017B030301016), and the Industry and Information Technology Foundation of Shenzhen (20180309100135860).

All experimentation using patient-derived gastric cancer stem cells described herein was approved by the local ethical committee7.
1. Gastric cancer stem cell culture
<ol>
	<li>Preparation of GCSCs complete culture medium
	<ol>
		<li>Prepare GCSCs complete culture medium by adding fresh DME/F12 medium with the following essential ingredients: 20 ng/mL EGF, 10 ng/mL bFGF, 1% Insulin/Transferrin/Sodium selenite, 0.2% glucose, 0.5% B27, 1% Glutamax, 1% Non-essential amin...

<ol>
	<li>Bray, 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=Global+cancer+statistics+2018:+GLOBOCAN+estimates+of+incidence+and+mortality+worldwide+for+36+cancers+in+185+countries.">Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.</a> CA: A Cancer Journal for Clinicians. 68 (6), 394-424 (2018).</li><li>Siegel, R. L., Miller, K. D., Jemal, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cancer+statistics,+2016.">Cancer statistics, 2016.</a> CA: A Cancer Journal for Clinicians. 66 (1), 7-30 (2016).</li><li>Valent, P., 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=Cancer+stem+cell+definitions+and+terminology:+the+devil+is+in+the+details.">Cancer stem cell definitions and terminology: the devil is in the details.</a> Nature Reviews Cancer. 12 (11), 767-775 (2012).</li><li>P&#252;tzer, B. M., Solanki, M., Herchenr&#246;der, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+cancer+stem+cell+targeting:+How+to+strike+the+evil+at+its+root.">Advances in cancer stem cell targeting: How to strike the evil at its root.</a> Advanced Drug Delivery Reviews. 120, 89-107 (2017).</li><li>Saygin, C., Matei, D., Majeti, R., Reizes, O., Lathia, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeting+Cancer+Stemness+in+the+Clinic:+From+Hype+to+Hope.">Targeting Cancer Stemness in the Clinic: From Hype to Hope.</a> Cell Stem Cell. 24 (1), 25-40 (2019).</li><li>Takaishi, 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=Identification+of+gastric+cancer+stem+cells+using+the+cell+surface+marker+CD44.">Identification of gastric cancer stem cells using the cell surface marker CD44.</a> Stem Cells. 27 (5), 1006-1020 (2009).</li><li>Chen, 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=Identification+and+expansion+of+cancer+stem+cells+in+tumor+tissues+and+peripheral+blood+derived+from+gastric+adenocarcinoma+patients.">Identification and expansion of cancer stem cells in tumor tissues and peripheral blood derived from gastric adenocarcinoma patients.</a> Cell Research. 22 (1), 248-258 (2012).</li><li>Pastrana, E., Silva-Vargas, V., Doetsch, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Eyes+wide+open:+a+critical+review+of+sphere-formation+as+an+assay+for+stem+cells.">Eyes wide open: a critical review of sphere-formation as an assay for stem cells.</a> Cell Stem Cell. 8 (5), 486-498 (2011).</li><li>Hannon, G. J., Rossi, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Unlocking+the+potential+of+the+human+genome+with+RNA+interference.">Unlocking the potential of the human genome with RNA interference.</a> Nature. 431 (7006), 371-378 (2004).</li><li>Seibler, J., 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=Reversible+gene+knockdown+in+mice+using+a+tight,+inducible+shRNA+expression+system.">Reversible gene knockdown in mice using a tight, inducible shRNA expression system.</a> Nucleic Acids Research. 35 (7), e54 (2007).</li><li>Xiong, J., 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=Verteporfin+blocks+Clusterin+which+is+required+for+survival+of+gastric+cancer+stem+cell+by+modulating+HSP90+function.">Verteporfin blocks Clusterin which is required for survival of gastric cancer stem cell by modulating HSP90 function.</a> International Journal of Biological Sciences. 15 (2), 312-324 (2019).</li><li>Ohkawa, J., Taira, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Control+of+the+functional+activity+of+an+antisense+RNA+by+a+tetracycline-responsive+derivative+of+the+human+U6+snRNA+promoter.">Control of the functional activity of an antisense RNA by a tetracycline-responsive derivative of the human U6 snRNA promoter.</a> Human Gene Therapy. 11 (4), 577-585 (2000).</li></ol>

GC is the third leading cause of cancer-related death worldwide. GCSCs are&#160;critical in gastric cancer relapse, metastasis and drug resistance. Using GCSCs from gastric cancer patients will allow us to explore their weak spot and develop the targeting drugs for the treatment of GC patients.
The sphere formation assay is a useful method to examine cancer stem cell self-renewal potential in vitro. Results can be presented as the percentage of spheres formed divided by the original number of ...

Gastric cancer (GC) is one of the most common and mortal types of cancers1. Despite advances in combined surgery, chemotherapy and radiotherapy in GC therapy, prognosis remains poor and the five-year survival rate is still very low2. Recurrence and metastasis are the main reasons cause the post-treatment deaths.
Cancer stem cells (CSCs) are a subset of cancer cells that possess the ability to self-renew and generate the different cell lineages that reconstitute the tumor3. CSCs are believed to be responsible for cancer relapse and metastasis because of their capabilities of self-renewal and seeding new tumors, as well as their resistance to traditional chemo- and radiotherapies4. Therefore, targeting CSCs and elimination of CSCs provide an exciting potential to improve the treatment and reduce mortality of cancer patients.
CSCs have been isolated from many types of solid tumors5. In 2009, gastric cancer stem cells (GCSCs) isolated from human gastric cancer cell lines were originally described by Takaishi et al.6. Chen and colleagues firstly identified and purified GCSCs from human gastric adenocarcinoma (GAC) tumor tissues7. These findings not only provide an opportunity to study GCSCs&#160;biology but also provide great clinical importance.
A particular characteristic of CSCs is their capacity to form a sphere8. Single cells are plated in nonadherent conditions at low density, and only the cells possessed with self-renewal can grow into a solid, spherical cluster called a sphere. Thus, the sphere formation assay has been regarded as the gold standard assay and widely used to evaluate stem cell self-renewal potential in vitro.
RNA interference (RNAi) is a powerful research tool to study gene function by the knockdown of a specific gene9. However, long term stable gene knockdown technologies have certain limitations, such as the challenge of exploring the function of a gene that is essential for cell survival. Conditional RNAi systems can be useful for the downregulation of desired genes in a temporal and/or special controlled manner by the administration of an inducing agent. The tetracycline (Tet)-inducible systems are one of the most widely used conditional RNAi systems10. The Tet-inducible systems can induce target gene silencing by controlling the expression of shRNA upon addition of an exogenous inducer (preferentially doxycycline, Dox). The Tet-inducible systems can be divided into two types: Tet-On or Tet-Off systems. The expression of shRNA can be turned on (Tet-On) or turned off (Tet-Off) in the presence of the inducer. In the Tet-ON system without an inducer, the constitutively expressed Tet repressor (TetR) binds to the Tet-responsive element (TRE) sequence containing a Tet-responsive Pol III-dependent promoter for shRNA expression, thus repressing the expression of the shRNA. While upon addition of Dox, the TetR is sequestered away from the Tet-responsive Pol III-dependent promoter. This facilitates the expression of the shRNA and leads to gene knockdown.
The protocol described here employs a functional tetracycline-inducible shRNA system and an adapted sphere formation assay to study the function of clusterin in patient-derived GCSCs. Clusterin has been identified as a novel key molecule for maintaining the stemness and survival of GCSCs in a previous study11. We use the described protocol to study the effects of clusterin in GCSCs&#160;self-renewal. This methodology is also applicable to other types of cancer stem cells.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.22 &#956;m filter</td>
			<td>Millipore</td>
			<td>SLGP033RB</td>
			<td></td>
		</tr>
		<tr>
			<td>1-Thioglycerol</td>
			<td>Sigma-Aldrich</td>
			<td>M6145</td>
			<td></td>
		</tr>
		<tr>
			<td>2-Mercaptoethanol</td>
			<td>Gibco</td>
			<td>2068586</td>
			<td></td>
		</tr>
		<tr>
			<td>Animal-Free Recombinant Human EGF</td>
			<td>Peprotech</td>
			<td>AF-100-15</td>
			<td></td>
		</tr>
		<tr>
			<td>B-27 Supplement (50X), serum free</td>
			<td>Gibco</td>
			<td>17504044</td>
			<td></td>
		</tr>
		<tr>
			<td>Corning Costar Ultra-Low Attachment Multiple Well Plate</td>
			<td>Sigma-Aldrich</td>
			<td>CLS3474</td>
			<td></td>
		</tr>
		<tr>
			<td>Countess Cell Counting Chamber Slides</td>
			<td>Invitrogen</td>
			<td>C10228</td>
			<td></td>
		</tr>
		<tr>
			<td>Countess II Automated Cell Counter</td>
			<td>Invitrogen</td>
			<td>AMQAX1000</td>
			<td></td>
		</tr>
		<tr>
			<td>D-(+)-Glucose</td>
			<td>Sigma-Aldrich</td>
			<td>G6152</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM/F-12, HEPES</td>
			<td>Gibco</td>
			<td>11330032</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM, High Glucose, GlutaMAX, Pyruvate</td>
			<td>Gibco</td>
			<td>10569044</td>
			<td></td>
		</tr>
		<tr>
			<td>Doxycycline hyclate</td>
			<td>Sigma-Aldrich</td>
			<td>D9891</td>
			<td></td>
		</tr>
		<tr>
			<td>DPBS, no calcium, no magnesium</td>
			<td>Gibco</td>
			<td>14190250</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum, qualified, Australia</td>
			<td>Gibco</td>
			<td>10099141</td>
			<td></td>
		</tr>
		<tr>
			<td>GlutaMAX Supplement</td>
			<td>Gibco</td>
			<td>35050061</td>
			<td></td>
		</tr>
		<tr>
			<td>Insulin, Transferrin, Selenium Solution (ITS -G), 100X</td>
			<td>Gibco</td>
			<td>41400045</td>
			<td></td>
		</tr>
		<tr>
			<td>lentiviral vector</td>
			<td>GeneChem</td>
			<td>GV307</td>
			<td></td>
		</tr>
		<tr>
			<td>Lenti-X Concentrator</td>
			<td>Takara</td>
			<td>631232</td>
			<td></td>
		</tr>
		<tr>
			<td>Lipofectamine 3000 Transfection Reagent</td>
			<td>Invitrogen</td>
			<td>L3000015</td>
			<td></td>
		</tr>
		<tr>
			<td>MEM Non-Essential Amino Acids Solution, 100X</td>
			<td>Gibco</td>
			<td>11140050</td>
			<td></td>
		</tr>
		<tr>
			<td>Millex-HV Syringe Filter Unit, 0.45 &#181;m, PVDF, 33 mm, gamma sterilized</td>
			<td>Millipore</td>
			<td>SLHV033RB</td>
			<td></td>
		</tr>
		<tr>
			<td>Nalgene General Long-Term Storage Cryogenic Tubes</td>
			<td>Thermo Scientific</td>
			<td>5000-1020</td>
			<td></td>
		</tr>
		<tr>
			<td>Nunc Cell Culture/Petri Dishes</td>
			<td>Thermo Scientific</td>
			<td>171099</td>
			<td></td>
		</tr>
		<tr>
			<td>Opti-MEM I Reduced Serum Medium</td>
			<td>Gibco</td>
			<td>31985070</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin, Liquid</td>
			<td>Gibco</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>pHelper 1.0 (gag/pol component)</td>
			<td>GeneChem</td>
			<td>pHelper 1.0</td>
			<td></td>
		</tr>
		<tr>
			<td>pHelper 2.0 (VSVG component)</td>
			<td>GeneChem</td>
			<td>pHelper 2.0</td>
			<td></td>
		</tr>
		<tr>
			<td>Polybrene</td>
			<td>Sigma-Aldrich</td>
			<td>H9268</td>
			<td></td>
		</tr>
		<tr>
			<td>Recombinant Human FGF-basic</td>
			<td>Peprotech</td>
			<td>100-18B</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium bicarbonate</td>
			<td>Sigma-Aldrich</td>
			<td>S5761</td>
			<td></td>
		</tr>
		<tr>
			<td>STEM-CELLBANKER Cryopreservation Medium</td>
			<td>ZENOAQ</td>
			<td>11890</td>
			<td></td>
		</tr>
		<tr>
			<td>StemPro Accutase Cell Dissociation Solution</td>
			<td>Gibco</td>
			<td>A1110501</td>
			<td></td>
		</tr>
		<tr>
			<td>UltraPure 1 M Tris-HCI Buffer, pH 7.5</td>
			<td>Invitrogen</td>
			<td>15567027</td>
			<td></td>
		</tr>
		<tr>
			<td>ZEISS Inverted Microscope</td>
			<td>ZEISS</td>
			<td>Axio Vert.A1</td>
			<td></td>
		</tr>
	</tbody>
</table>

combined conditional knockdown and adapted sphere formation assay to study a stemness-associated gene of patient-derived gastric cancer stem cells

Cancer stem cells (CSCs) are implicated in tumor initiation, development and recurrence after treatment, and have become the center of attention of many studies in the last decades. Therefore, it is important to develop methods to investigate the role of key genes involved in cancer cell stemness. Gastric cancer (GC) is one of the most common and mortal types of cancers. Gastric cancer stem cells (GCSCs) are thought to be the root of gastric cancer relapse, metastasis and drug resistance. Understanding GCSCs&#160;biology is needed to advance the development of targeted therapies and eventually to reduce mortality among patients. In this protocol, we present an experimental design using a conditional knockdown system and an adapted sphere formation assay to study the effect of clusterin on the stemness of patient-derived GCSCs. The protocol can be easily adapted to study both in vitro and in vivo function of stemness-associated genes in different types of CSCs.

Gastric cancer stem cells from primary human gastric adenocarcinoma were cultured in serum-free culture medium. After 6 days, cells expanded from the single cell-like phenotype (Figure 1A) to form large spheres (Figure 1B).
To assess the function of clusterin in GCSCs, shRNA sequences against clusterin and scrambled were cloned into Tet...

Watch this Scientific Journal Video about Combined Conditional Knockdown and Adapted Sphere Formation Assay to Study a Stemness-Associated Gene of Patient-derived Gastric Cancer Stem Cells at JoVE.com

Combined Conditional Knockdown and Adapted Sphere Formation Assay to Study a Stemness-Associated Gene of Patient-derived Gastric Cancer Stem Cells

In this protocol, we present an experimental design using a conditional knockdown system and an adapted sphere formation assay to study the effect of clusterin on the stemness of patient-derived GCSCs. The protocol can be easily adapted to study both in vitro and in vivo function of stemness-associated genes in different types of CSCs.

Cancer stem cells (CSCs) are implicated in tumor initiation, development and recurrence after treatment, and have become the center of attention of many ...

Cancer stem cells are implicated in cancer relapsed metastasis on drug resistance. This protocol provides an efficient method for investigating the functions of key genes in cancer stem cells. Using a conditional knockdown system and adapted sphere formation assay, this method is easily adapted to study in vitro and in vivo functions on stemness-associated genes in different types of cancer stem cells.Demonstrating the procedure, will be Yuting Li and Xiangyu Tan, research assistants from my laboratory. To generate lentivirus particles, seed four million 293T lentiviral packaging cells into a 100 millimeter Petri dish with 10 milliliters of DMEM supplemented with 10%FBS. Incubate the cells overnight at 37 degrees Celsius and 5%carbon dioxide, making sure that the cells are 50 to 80%confluent on the day of transfection.Bring reduced serum medium to room temperature and prepare tubes A and B according to manuscript directions. Add the contents of tube A to tube B.Mix well and incubate the tube for 15 minutes at room temperature to prepare lipid-DNA complexes. Remove five milliliters of medium from the cell culture dish.Then add five milliliters of the lipid-DNA complex into the cell culture dish drop wise and gently swirl the dish. Incubate the culture dish for 24 hours at 37 degrees Celsius and 5%carbon dioxide. After the incubation, carefully remove the transfection medium and replace it with 10 milliliters of pre-warmed DMEM supplemented with 10%FBS.Incubate the cells for another 24 hours. Approximately 48 hours post transfection, harvest 10 milliliters of lentivirus containing supernatants and filter them with a 0.45 micrometer pour filter to remove cellular debris. All the cell culture vessels, tips, filters and syringes may contain lentivirus and should be treated with 10%bleach prior to disposal.Transfer a clarified supernatant to a sterile container. Add Lenti-X concentrator and mix with gentle inversion. Incubate the mixture at four degrees Celsius overnight.On the next day, centrifuge the sample at 1500 times G for 45 minutes at four degrees Celsius. Carefully remove the supernatant, taking care not to disturb the pellet at the bottom. Gently re-suspend the pellet in one milliliter of DMEM supplemented with 10%FBS and store it at minus 80 degrees Celsius.Seed 6 million gastric cancer stem cells or GCSC's into a 100 millimeter Petri dish with 10 milliliters of DMEM supplemented with 10%FBS. Culture the cells for 24 hours at 37 degrees Celsius and 5%carbon dioxide. When the cells reach 70 to 80%confluency, aspirate the medium from the dish and add the concentrated lentiviral particles diluted with four millimeters of complete DMEM medium, containing Polybrene reagent.Return the cells to the incubator for 18 hours. Polybrene should be tested in different conditions to determine the effective concentration, which is usually in the range of two to 10 milligram per milliliter. After 18 hours, replace the medium with 10 milliliters of DMEM with 10%FBS and return the cells to the incubator for 24 hours.Then, aspirate the supernatant with the cell debris and add fresh DMEM supplemented with 10%FBS and 2.5 micrograms per milliliter of Puromycin. Incubate the cells for another 24 hours. Then, change the medium again to fresh DMEM supplemented with 10%FBS and five micrograms per milliliter Puromycin.After another 24 hour incubation, rinse the adherent GCSCs twice with five milliliters of DPBS without calcium and magnesium. Dissociate the cells with one milliliter of pre-warmed cell dissociation solution and incubate them for two to three minutes at 37 degrees Celsius. Then, add five milliliters of fresh pre-warmed GCSC complete culture medium to the cell suspension.Dispense three milliliters of this suspension into a 15 milliliter centrifuge tube for cryopreservation, and the other three milliliters into another tube for induction with doxycycline. Centrifuge both tubes at 800 times G for five minutes. Then, aspirate the supernatant from tube B and re-suspend the cells in one milliliter of fresh pre-warmed GCSC complete culture medium.Seed an appropriate number of cells into a new 100 millimeter Petri dish with 10 milliliters of fresh pre-warmed GCSC complete culture medium and 2.5 micrograms per milliliter doxycycline. Then, incubate the dish for 48 hours. Use an automated cell counter to determine the density of a 10 microliter sample of cells.Then, adjust the volume with pre-warmed GCSC complete culture medium to obtain a concentration of 20, 000 viable cells per milliliter. Dispense 100 microliters of the cell suspension into each well of a new, ultra low attachment 96 well culture plate. Incubate the cells at 37 degrees Celsius with 5%carbon dioxide.Sphere formation should occur within three to 10 days. Image the tumor sphere formation every two days. Gastric cancer stem cells from primary human gastric adenocarcinoma were cultured in serum free culture medium.After six days, cells expanded from the single-cell like phenotype to large spheres. To assess the function of clusterin in GCSCs, short hairpin RNA sequences against clusterin were cloned into the Tet-GV307-RFP-Puro vector. Cells transfected with the expression vector were treated with doxycycline for 48 hours.Then, clusterin expression was verified by Western blot and quantified by densitometry. The presence of doxycycline and knockdown of clusterin in GCSCs inhibited tumor sphere formation. While no inhibition of tumor sphere formation was observed in cells transduced with the scrambled shRNA controls, indicating that doxycycline alone did not inhibit tumor sphere formation.These results suggest that after clusterin silencing, GCSCs grow slowly and cannot form tumor spheres. Based on this data, clusterin plays a critical role in promoting the self-renewal activity of GCSCs, indicating that it could be a promising drug target for suppressing cancer stem cells in gastric cancer patients. The tumors spheres should be solid round structures on individual or aggregated cells, should not be considered tumor spheres.However, some cancer stem cells may not form typical tumor sphere structures. This procedure can be followed with other methods to examine cancer stem cell for renewable potential in vitro. For example, the expression of stemness-related markers can be studied.The protocol can be extended to study the functions of the critical genes in cancer stem cells such as stemness on survival.

Combined Conditional Knockdown and Adapted Sphere Formation Assay to Study a Stemness-Associated Gene of Patient-derived Gastric Cancer Stem Cells

Abstract