This work was supported by The National Institutes of Health (R35GM133581 to JC) and the Cancer Center at Illinois Graduate Scholarship (awarded to SG). JC thanks the Camille and Henry Dreyfus Foundation for support. The authors thank Dr. Thomas E. Bearrood for his initial contribution to preparing stocks of AlDeSense and AlDeSense AM. We thank Mr. Oliver D. Pichardo Peguero and Mr. Joseph A. Forzano for their assistance with preparing various synthetic precursors. We thank Prof. Erik Nelson (Department of Molecular and Integrative Physiology, UIUC) for Caov-3, IGROV-1, and PEO4 cells. We thank Prof. Paul Hergenrother (Department of Chemistry, UIUC) for BG-1 cells. We thank the Core Facilities at the Carl R. Woese Institute for Genomic Biology for access to the Zeiss LSM 700 Confocal Microscope and corresponding software. We thank the Flow Cytometry Facility for access to BD LSR II CMtO Analyzer. We thank Dr. Sandra McMasters and the Cell Media Facility for assistance in preparing cell culture media.

1. Measure total ALDH1A1 activity in ovarian cancer cell homogenates via fluorimetry
<ol>
	<li>Thaw 1 &#215; 106 cells in a T25 cell culture flask in 5 mL of the following cell culture media:
	<ol>
		<li>IGROV-1 and PEO4: Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S).</li>
		<li>BG-1 and Caov-3: Dulbecco&#39;s Modified Eagle&#39;s Medium (DMEM) with 10% FBS and 1% P/S.</li>
		<li>OVCAR-3: RPMI 1640 with 20% FBS, 1% P/S, and 0.01 mg/mL insulin.</li>
	</ol>
	</li>
	<li>Maintain the cells in an incubator at 37 &#176;C and 5% CO2 for two to three passages. Ensure the cells do not exceed 80%-90% confluency before passaging.</li>
	<li>Trypsinize the cells in 0.25% trypsin for 10 min, count them using an automated cell counter, and pellet 1 &#215; 107 cells via centrifugation (180 &#215; g) at 25 &#176;C for 5 min.</li>
	<li>Remove the supernatant carefully via aspiration, wash the pellet by resuspending the cells in 1 mL of 1x PBS, and re-pellet the cells via centrifugation under the same conditions as described in step 4.</li>
	<li>Resuspend the cells in a solution of 1x protease inhibitor in 1x PBS. Use 1 mL of this solution per 2.5 &#215; 106 cells.</li>
	<li>Sonicate the cell suspension on ice for 2 min (1 s pulse, 40% amplitude) with a cell homogenizer probe.</li>
	<li>Pellet insoluble/membrane fractions via centrifugation (3,200 &#215; g) at 25 &#176;C for 15 min. Remove and keep the supernatant, as this is the homogenate that will be used in subsequent steps. Separate the homogenates into three cuvettes to perform the experiment in triplicate.</li>
	<li>Add the probe to the homogenate to obtain a final probe concentration of 4 &#181;M. Pipette up and down three times to mix the solution well.</li>
	<li>Measure the fluorescent signal immediately after addition and after desired incubation times on a fluorimeter. The incubation time can be optimized to see the maximum fold turn-on (1 h in this experiment). The incubation time must be constant across all cell lines compared.
	<ol>
		<li>Set the excitation wavelength to 496 nm.</li>
		<li>Set the emission to 510-600 nm.</li>
		<li>Set the slit width to 0.5 mm.</li>
		<li>Pipette the solution into a 1 mL quartz cuvette, place into the fluorimeter, and hit scan.</li>
	</ol>
	</li>
	<li>Divide the final fluorescence intensity at 516 nm (maximum fluorescent wavelength) by the intensity at the same wavelength from the initial reading to determine the fold activation of the isoform-selective dye.</li>
</ol>
2. Use of fluorescence microscopy to image cells with high ALDH1A1 activity
<ol>
	<li>Thaw 1 &#215; 106 cells in a T25 cell culture flask in 5 mL of the appropriate cell culture media.</li>
	<li>Maintain the cells in an incubator at 37 &#176;C and 5% CO2 for two to three passages. Ensure the cells do not exceed 80%-90% confluency before passaging.</li>
	<li>The day prior to confocal imaging, plate 4 &#215; 105 cells in an 8-well chamber slide.
	<ol>
		<li>Coat the bottom of each well with poly-L-lysine (0.1 mg/mL, 100 &#181;L per well) for 10 min, subsequently aspirating.</li>
		<li>Wash each well 3x by adding cell culture grade water (100 &#181;L per well) and aspirating.</li>
		<li>Trypsinize the cells in 0.25% trypsin for 10 min, count them using an automated cell counter, and plate the cells at 4 &#215; 105 cells per well.</li>
		<li>Let the cells settle and attach overnight (12-16 h).</li>
	</ol>
	</li>
	<li>Aspirate the growth media and add serum-free media (500 &#181;L per well), supplemented with&#160;2 &#181;M of the probe or the&#160;control probe.</li>
	<li>Incubate with the probe at room temperature for 30 min and image the cells immediately.</li>
	<li>Turn on the confocal microscope and adjust for the sample.
	<ol>
		<li>Load the sample carefully at the lowest magnification; find the cells to ensure proper positioning.</li>
		<li>Ensure the objective lens is at 10x magnification and locate the cells.</li>
	</ol>
	</li>
	<li>For this experiment, the FITC channel (excitation: 488 nm laser; emission: 516-521 nm) and T-PMT (transmitted light) channel are required. Locate and focus on the cells using T-PMT to focus on the same z-plane for the entirety of the experiment to remove bias.</li>
	<li>Adjust the laser power and FITC gain to the appropriate setting, where the signal from the Ctrl-AlDeSense AM samples is minimally detectable, while still seeing signal in AlDeSense AM samples. Each parameter can be adjusted by sliding the corresponding bar. The settings may have to be adjusted a few times to identify the correct parameters. Once optimized, complete the rest of the experiment within that cell line using identical parameters.</li>
	<li>Snap three images per well for a total of three wells per treatment condition (nine images in total). Focus on the proper plane using T-PMT to avoid bias rather than using the fluorescence channel or merged image.</li>
	<li>Process the images to determine the percentage of ALDH1A1+ cells.
	<ol>
		<li>Using image processing software, split the czi file into different channels.</li>
		<li>Count the total number of cells and the total number of fluorescent cells.</li>
		<li>To determine the percentage of ALDH1A1+ cells, divide the number of fluorescent cells by the total number of cells in each image. It is imperative to count the same way for each image without manipulating the images, as, for instance, adjusting the brightness may add a confounding variable.</li>
	</ol>
	</li>
</ol>
3. Application of flow cytometry to identify cells with high ALDH1A1 activity
<ol>
	<li>Thaw 1 &#215; 106 cells in a T25 cell culture flask in 5 mL of the appropriate cell culture media.</li>
	<li>Maintain the cells in an incubator at 37 &#176;C and 5% CO2 for two to three passages. Ensure the cells do not exceed 80%-90% confluency before passaging.</li>
	<li>Trypsinize, count, and pellet the cells in a 15 mL centrifuge tube via centrifugation (180 &#215; g) at 25 &#176;C for 5 min.</li>
	<li>Resuspend the cells in 1 mL of 2 &#181;M probe/control probe solution in PBS. Rock the cells at room temperature for 60 min to ensure exposure to the dye is even.</li>
	<li>After the incubation period, pellet the cells via centrifugation (180 &#215; g) at 25 &#176;C for 5 min. Resuspend the cells in 0.5 mL of PBS. Run the cells through a cell strainer (35 &#181;m nylon mesh) to remove cell clumps that may clog the flow cytometer. Immediately place the cells on ice.</li>
	<li>Turn the instrument on and run the start-up protocol.</li>
	<li>Check for sheath fluid and empty waste.</li>
	<li>Run the lines with 10% bleach and water for 5 min each.</li>
	<li>Run quality control beads to ensure proper function.</li>
	<li>In the settings tab, select FSC (forward scatter), SSC (side scatter), and FITC (fluorescein isothiocyanate) for the fluorescence filter.</li>
	<li>Draw the following graphs to gate for viability, singlets, and fluorescence. Optimize the laser power (specific to user&#39;s instrument) so that the cell populations are within the given parameters for further analysis.
	<ol>
		<li>FSC-A versus SSC-A scatter plot: main cell population is near the center of the graph.</li>
		<li>FSC-A versus FSC-W scatter plot: narrow horizontal band indicative of singlets (rather than cell clumps).</li>
		<li>FITC-A versus FSC-A scatter plot: observe the distribution of cells sorted by the isoform-selective fluorogenic turn-on probe.</li>
		<li>FITC-A histogram: observe the shift in population based on FITC to determine the percentage of ALDH1A1+ cells.</li>
	</ol>
	</li>
	<li>To optimize the FITC laser power, run a sample with the probe so that the right tail of the histogram curve is near the maximum FITC-A signal. Subsequently, run a sample with the control probe. A population shift should be observable to reveal the maximum dynamic range. The laser power optimization step may have to be repeated multiple times, but the laser power should not be altered across samples once a setting has been designated for an experiment.</li>
	<li>Run each sample for 10,000 counts (done in triplicate).</li>
	<li>Repeat step 3.12 for each cell line, as there will be variability in uptake and ALDH1A1 activity.</li>
	<li>After completion of sample collection, run the lines with 10% bleach and water for 5 min each, then initiate shutdown of the instrument.</li>
	<li>Process the data using the flow cytometry software and gate the desired cell population. Set the gates so that all events fall into either the ALDH1A1- or ALDH1A1+ gate. Using the rectangle gate selection, set the ALDH1A1- gate so that &#62;99.5% of events in the control probe samples occur within this gate. The remaining cells will be considered ALDH1A1+. These same gates can then be applied to the probe sample to quantify the number of events considered ALDH1A1- and ALDH1A1+.</li>
</ol>

<ol>
	<li>Bonnet, D., Dick, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+acute+myeloid+leukaemia+is+organised+as+a+heirarchy+that+originates+from+a+primitive+haematopoetic+cell.">Human acute myeloid leukaemia is organised as a heirarchy that originates from a primitive haematopoetic cell.</a> Nature Medicine. 3 (7), 730-737 (1997).</li><li>Begicevic, R. R., Falasca, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ABC+transporters+in+cancer+stem+cells:+Beyond+chemoresistance.">ABC transporters in cancer stem cells: Beyond chemoresistance.</a> International Journal of Molecular Sciences. 18 (11), 2362 (2017).</li><li>Cojoc, M., M&#228;bert, K., Muders, M. H., Dubrovska, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+role+for+cancer+stem+cells+in+therapy+resistance:+Cellular+and+molecular+mechanisms.">A role for cancer stem cells in therapy resistance: Cellular and molecular mechanisms.</a> Seminars in Cancer Biology. 31, 16-27 (2015).</li><li>Islam, F., Gopalan, V., Smith, R. A., Lam, A. K. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Translational+potential+of+cancer+stem+cells:+A+review+of+the+detection+of+cancer+stem+cells+and+their+roles+in+cancer+recurrence+and+cancer+treatment.">Translational potential of cancer stem cells: A review of the detection of cancer stem cells and their roles in cancer recurrence and cancer treatment.</a> Experimental Cell Research. 335 (1), 135-147 (2015).</li><li>Li, F., Tiede, B., Massagu&#233;, J., Kang, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Beyond+tumorigenesis:+Cancer+stem+cells+in+metastasis.">Beyond tumorigenesis: Cancer stem cells in metastasis.</a> Cell Research. 17 (1), 3-14 (2007).</li><li>Kim, W. T., Ryu, C. J. <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+surface+markers+on+normal+stem+cells.">Cancer stem cell surface markers on normal stem cells.</a> BMB Reports. 50 (6), 285-298 (2017).</li><li>Pors, K., Moreb, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aldehyde+dehydrogenases+in+cancer:+An+opportunity+for+biomarker+and+drug+development.">Aldehyde dehydrogenases in cancer: An opportunity for biomarker and drug development.</a> Drug Discovery Today. 19 (12), 1953-1963 (2014).</li><li>Jackson, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Update+on+the+aldehyde+dehydrogenase+gene+(ALDH)+superfamily.">Update on the aldehyde dehydrogenase gene (ALDH) superfamily.</a> Human Genomics. 5 (4), 283-303 (2011).</li><li>Vasiliou, V., Pappa, A., Petersen, D. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+aldehyde+dehydrogenases+in+endogenous+and+xenobiotic+metabolism.">Role of aldehyde dehydrogenases in endogenous and xenobiotic metabolism.</a> Chemico-Biological Interactions. 129 (1-2), 1-19 (2000).</li><li>Tomita, H., Tanaka, K., Tanaka, T., Hara, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aldehyde+dehydrogenase+1A1+in+stem+cells+and+cancer.">Aldehyde dehydrogenase 1A1 in stem cells and cancer.</a> Oncotarget. 7 (10), 11018-11032 (2016).</li><li>Anorma, 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=Surveillance+of+cancer+stem+cell+plasticity+using+an+isoform-selective+fluorescent+probe+for+aldehyde+dehydrogenase+1A1.">Surveillance of cancer stem cell plasticity using an isoform-selective fluorescent probe for aldehyde dehydrogenase 1A1.</a> ACS Central Science. 4 (8), 1045-1055 (2018).</li><li>Bearrood, T. E., Aguirre-Figueroa, G., Chan, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rational+design+of+a+red+fluorescent+sensor+for+ALDH1A1+displaying+enhanced+cellular+uptake+and+reactivity.">Rational design of a red fluorescent sensor for ALDH1A1 displaying enhanced cellular uptake and reactivity.</a> Bioconjugate Chemistry. 31 (2), 224-228 (2020).</li><li>Chan, J., Dodani, S. C., Chang, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reaction-based+small-molecule+fluorescent+probes+for+chemoselective+bioimaging.">Reaction-based small-molecule fluorescent probes for chemoselective bioimaging.</a> Nature Chemistry. 4 (12), 973-984 (2012).</li><li>East, A. K., Lucero, M. Y., Chan, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+directions+of+activity-based+sensing+for+in+vivo+NIR+imaging.">New directions of activity-based sensing for in vivo NIR imaging.</a> Chemical Science. 12 (10), 3393-3405 (2021).</li><li>Yadav, A. 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=Activity-based+NIR+bioluminescence+probe+enables+discovery+of+diet-induced+modulation+of+the+tumor+microenvironment+via+nitric+oxide.">Activity-based NIR bioluminescence probe enables discovery of diet-induced modulation of the tumor microenvironment via nitric oxide.</a> ACS Central Science. 8 (4), 461-472 (2022).</li><li>Yadav, A. 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=An+activity-based+sensing+approach+for+the+detection+of+cyclooxygenase-2+in+Live+Cells.">An activity-based sensing approach for the detection of cyclooxygenase-2 in Live Cells.</a> Angewandte Chemie. 59 (8), 3307-3314 (2020).</li><li>Ueno, 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=Rational+principles+for+modulating+fluorescence+properties+of+fluorescein.">Rational principles for modulating fluorescence properties of fluorescein.</a> Journal of the American Chemical Society. 126 (43), 14079-14085 (2004).</li><li>Tanaka, F., Mase, N., Barbas 3rd, C. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+and+use+of+fluorogenic+aldehydes+for+monitoring+the+progress+of+aldehyde+transformations.">Design and use of fluorogenic aldehydes for monitoring the progress of aldehyde transformations.</a> Journal of the American Chemical Society. 126 (12), 3692-3693 (2004).</li><li>Thurber, G. M., Schmidt, M. M., Wittrup, K. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Antibody+tumor+penetration:+transport+opposed+by+systemic+and+antigen-mediated+clearance.">Antibody tumor penetration: transport opposed by systemic and antigen-mediated clearance.</a> Advanced Drug Delivery Reviews. 60 (12), 1421-1434 (2008).</li><li>Marcato, P., Dean, C. A., Giacomantonio, C. A., Lee, P. W. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aldehyde+dehydrogenase+its+role+as+a+cancer+stem+cell+marker+comes+down+to+the+specific+isoform.">Aldehyde dehydrogenase its role as a cancer stem cell marker comes down to the specific isoform.</a> Cell Cycle. 10 (9), 1378-1384 (2011).</li><li>Meng, E., 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=ALDH1A1+maintains+ovarian+cancer+stem+cell-like+properties+by+altered+regulation+of+cell+cycle+checkpoint+and+DNA+repair+network+signaling.">ALDH1A1 maintains ovarian cancer stem cell-like properties by altered regulation of cell cycle checkpoint and DNA repair network signaling.</a> PLoS One. 9 (9), e107142 (2014).</li><li>Kaipio, 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=ALDH1A1-related+stemness+in+high-grade+serous+ovarian+cancer+is+a+negative+prognostic+indicator+but+potentially+targetable+by+EGFR/mTOR-PI3K/aurora+kinase+inhibitors.">ALDH1A1-related stemness in high-grade serous ovarian cancer is a negative prognostic indicator but potentially targetable by EGFR/mTOR-PI3K/aurora kinase inhibitors.</a> The Journal of Pathology. 250 (2), 159-169 (2020).</li><li>Deng, 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=Distinct+expression+levels+and+patterns+of+stem+cell+marker,+aldehyde+dehydrogenase+isoform+1+(ALDH1),+in+human+epithelial+cancers.">Distinct expression levels and patterns of stem cell marker, aldehyde dehydrogenase isoform 1 (ALDH1), in human epithelial cancers.</a> PLoS One. 5 (4), e10277 (2010).</li><li>Chang, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ALDH1+expression+correlates+with+favorable+prognosis+in+ovarian+cancers.">ALDH1 expression correlates with favorable prognosis in ovarian cancers.</a> Modern Pathology. 22 (6), 817-823 (2009).</li><li>Gardner, S. H., Reinhardt, C. J., Chan, J. <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+activity-based+sensing+probes+for+isoform-selective+imaging+of+enzymatic+activity.">Advances in activity-based sensing probes for isoform-selective imaging of enzymatic activity.</a> Angewandte Chemie. 60 (10), 5000-5009 (2021).</li><li>Reid, B. M., Permuth, J. B., Sellers, T. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epidemiology+of+ovarian+cancer:+a+review.">Epidemiology of ovarian cancer: a review.</a> Cancer Biology and Medicine. 14 (1), 9-32 (2017).</li><li>Tulake, W., 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=Upregulation+of+stem+cell+markers+ALDH1A1+and+OCT4+as+potential+biomarkers+for+the+early+detection+of+cervical+carcinoma.">Upregulation of stem cell markers ALDH1A1 and OCT4 as potential biomarkers for the early detection of cervical carcinoma.</a> Oncology Letters. 16 (5), 5525-5534 (2018).</li><li>Nwani, N. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+ALDH1A1+inhibitor+targets+cells+with+stem+cell+characteristics+in+ovarian+cancer.">A novel ALDH1A1 inhibitor targets cells with stem cell characteristics in ovarian cancer.</a> Cancers. 11 (4), 502 (2019).</li><li>Roy, M., Connor, J., Al-Niaimi, A., Rose, S. L., Mahajan, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aldehyde+dehydrogenase+1A1+(ALDH1A1)+expression+by+immunohistochemistry+is+associated+with+chemo-refractoriness+in+patients+with+high-grade+ovarian+serous+carcinoma.">Aldehyde dehydrogenase 1A1 (ALDH1A1) expression by immunohistochemistry is associated with chemo-refractoriness in patients with high-grade ovarian serous carcinoma.</a> Human Pathology. 73, 1-6 (2018).</li><li>Landen Jr, C. N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeting+aldehyde+dehydrogenase+cancer+stem+cells+in+ovarian+cancer.">Targeting aldehyde dehydrogenase cancer stem cells in ovarian cancer.</a> Molecular Cancer Therapeutics. 9 (12), 3186-3199 (2010).</li><li>Condello, 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=&#946;-catenin-regulated+ALDH1A1+is+a+target+in+ovarian+cancer+spheroids.">&#946;-catenin-regulated ALDH1A1 is a target in ovarian cancer spheroids.</a> Oncogene. 34 (18), 2297-2308 (2015).</li><li>Storms, R. W., 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=Isolation+of+primitive+human+hematopoietic+progenitors+on+the+basis+of+aldehyde+dehydrogenase+activity.">Isolation of primitive human hematopoietic progenitors on the basis of aldehyde dehydrogenase activity.</a> Proceedings of the National Academy of Sciences. 96 (16), 9118-9123 (1999).</li><li>Duellman, S. 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=A+bioluminescence+assay+for+aldehyde+dehydrogenase+activity.">A bioluminescence assay for aldehyde dehydrogenase activity.</a> Analytical Biochemistry. 434 (2), 226-232 (2013).</li><li>Minn, I., 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=A+red-shifted+fluorescent+substrate+for+aldehyde+dehydrogenase.">A red-shifted fluorescent substrate for aldehyde dehydrogenase.</a> Nature Communications. 5, 3662 (2014).</li><li>Doll&#233;, L., Boulter, L., Leclercq, I. A., van Grunsven, L. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Next+generation+of+ALDH+substrates+and+their+potential+to+study+maturational+lineage+biology+in+stem+and+progenitor+cells.">Next generation of ALDH substrates and their potential to study maturational lineage biology in stem and progenitor cells.</a> American Journal of Physiology. Gastrointestinal and Liver Physiology. 308 (7), 573-578 (2015).</li><li>Yagishita, 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=Development+of+highly+selective+fluorescent+probe+enabling+flow-cytometric+isolation+of+ALDH3A1-positive+viable+cells.">Development of highly selective fluorescent probe enabling flow-cytometric isolation of ALDH3A1-positive viable cells.</a> Bioconjugate Chemistry. 28 (2), 302-306 (2017).</li><li>Maity, 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=Thiophene+bridged+aldehydes+(TBAs)+image+ALDH+activity+in+cells:+Via+modulation+of+intramolecular+charge+transfer.">Thiophene bridged aldehydes (TBAs) image ALDH activity in cells: Via modulation of intramolecular charge transfer.</a> Chemical Science. 8 (10), 7143-7151 (2017).</li><li>Koenders, S. T. 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=Development+of+a+retinal-based+probe+for+the+profiling+of+retinaldehyde+dehydrogenases+in+cancer+cells.">Development of a retinal-based probe for the profiling of retinaldehyde dehydrogenases in cancer cells.</a> ACS Central Science. 5 (12), 1965-1974 (2019).</li><li>Oe, 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=Deep-red/near-infrared+turn-on+fluorescence+probes+for+aldehyde+dehydrogenase+1A1+in+cancer+stem+cells.">Deep-red/near-infrared turn-on fluorescence probes for aldehyde dehydrogenase 1A1 in cancer stem cells.</a> ACS Sensors. 6 (9), 3320-3329 (2021).</li><li>Yagishita, A., Ueno, T., Tsuchihara, K., Urano, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Amino+BODIPY-based+blue+fluorescent+probes+for+aldehyde+dehydrogenase+1-expressing+cells.">Amino BODIPY-based blue fluorescent probes for aldehyde dehydrogenase 1-expressing cells.</a> Bioconjugate Chemistry. 32 (2), 234-238 (2021).</li><li>Okamoto, 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=Identification+of+breast+cancer+stem+cells+using+a+newly+developed+long-acting+fluorescence+probe,+C5S-A,+targeting+ALDH1A1.">Identification of breast cancer stem cells using a newly developed long-acting fluorescence probe, C5S-A, targeting ALDH1A1.</a> Anticancer Research. 42 (3), 1199-1205 (2022).</li></ol>

We disclose a pending patent (US20200199092A1) for the AlDeSense technology.

Pan-selectivity is a major limitation of many ALDH probes; however, several isoform-selective examples have recently been reported32,33,34,35,36,37,38,39,40,41. The isoform-selective fluo...

Cancer stem cells (CSCs) are a subpopulation of tumor cells that exhibit stem cell-like properties1. Similar to their non-cancerous counterparts, CSCs possess the extraordinary ability to self-renew and proliferate. Together with other built-in mechanisms, such as the upregulation of ATP-binding cassette transporters, CSCs are often spared from initial surgical debulking efforts, as well as subsequent adjuvant therapy2. Owing to their critical role in treatment resistance3, relapse4, and metastasis5, CSCs have become a priority in cancer research. Although there are a variety of cell surface antigens (e.g., CD133) that can be used to identify CSCs6, leveraging the enzymatic activity of aldehyde dehydrogenases (ALDHs) found in the cytoplasm has emerged as an attractive alternative7. ALDHs are a superfamily of 19 enzymes responsible for catalyzing the oxidation of reactive endogenous and xenobiotic aldehydes to the corresponding carboxylic acid products8.
In general, aldehyde detoxification is crucial in protecting cells from undesirable crosslinking events and oxidative stress that may damage stem cell integrity9. Moreover, the 1A1 isoform controls retinoic acid metabolism, which in turn influences stemness via retinaldehyde signaling10. AlDeSense11,12, a small-molecule activity-based sensing (ABS) probe to selectively detect ALDH1A1 activity, was recently developed. ABS designs achieve analyte detection through a chemical change rather than a binding event, allowing for high selectivity and decreased off-target responses13,14,15,16. The design principle of the isoform-selective fluorogenic probe relies on a donor-photoinduced electron transfer (d-PeT) quenching mechanism17, originating from the aldehyde functional group, which serves to suppress the fluorescent signature of the probe18. Upon ALDH1A1-mediated conversion to the carboxylic acid, radiative relaxation is unlocked to yield a highly fluorescent product. Because d-PeT quenching is never 100% efficient, the residual fluorescence that may lead to possible false positive results was considered when establishing this assay through the development of Ctrl-AlDeSense, a non-responsive reagent with matching photophysical characteristics (e.g., quantum yield) and an identical cytoplasmic staining pattern in cells. When used in tandem, this unique pairing can reliably distinguish cells with high ALDH1A1 activity from those that exhibit low levels via fluorimetry, molecular imaging, and flow cytometry. Several key advantages are associated with the use of isoform-selective activatable dyes over traditional immunohistochemical methods. For instance, CSCs are hypothesized to be buried deep within a tumor, and thus are more accessible to a small molecule relative to large antibodies19. Additionally, the turned-over fluorescent product does not covalently modify any cellular component, meaning it can be readily removed via wash cycles to leave a CSC in an unmodified state. Lastly, the turn-on response only identifies viable cells and functions, much like the MTT assay, owing to its reliance on the NAD+ cofactor.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/64713/64713fig01.jpg" /> 
Figure 1: Schematic demonstrating fluorescent turn-on of AlDeSense. The isoform-selective dye is activated by ALDH1A1 and can be used to identify elevated ALDH1A1 activity in ovarian cancer cells via fluorimetry, molecular imaging, and flow cytometry. <a href="https://www.jove.com/files/ftp_upload/64713/64713fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
In past work, the isoform-selective fluorogenic probe assay successfully stratified ALDH high (ALDH+) cells from ALDH low (ALDH-) cells in K562 human chronic leukemia cells, MDA-MB-231 human breast cancer cells, and B16F0 murine melanoma cells. This is important because, for many cancer types, high ALDH1A1 protein expression signifies a worse clinical prognosis20. This presumes that elevated levels of ALDH1A1 are indicative of CSCs which can evade treatment, develop resistance, and disseminate throughout the body. However, in the case of ovarian cancer, there are studies reporting the opposite finding (high ALDH1A1 expression is linked to improved patient survival)21,22,23,24. While this may appear contradictory at first glance, expression does not necessarily correlate to enzyme activity, which may be influenced by changes in the tumor microenvironment (e.g., pH flux, oxygen gradients), availability of the NAD+ cofactor or aldehyde substrates, levels of carboxylic acids (product inhibition), and post-translational modifications that can alter enzyme activity25. Additionally, ovarian cancer is divided into five main histological types (high-grade serous, low-grade serous, endometrioid, clear cell, and mucinous), which we hypothesize will feature variable levels of ALDH1A1 activity26. With the goal of investigating ALDH1A1 activity in ovarian tumors, an isoform-selective fluorogenic probe assay was employed to identify ALDH1A1+ populations in a panel of five ovarian cancer cell lines belonging to the different histological types mentioned above. The cell lines tested in this study include BG-1, Caov-3, IGROV-1, OVCAR-3, and PEO4 cells, covering clear cell and serous histotypes. Herein, the versatility and generalizability of the probe was highlighted to identify CSCs for the researchers that seek to perform similar studies in other immortalized cancer cell lines as well as patient samples. The use of AlDeSense will shed light on the biochemical pathways involved in CSC maintenance in complex tissue microenvironments and potentially serve as a clinical tool for determining prognosis and measuring cancer aggressiveness.

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			<td>&#160;0.25% Trypsin, 0.1% EDTA in HBSS w/o Calcium, Magnesium and Sodium Bicarbonate</td>
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			<td>1x Phosphate Buffer Saline</td>
			<td>Corning</td>
			<td>21-040-CMX12</td>
			<td></td>
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			<td>AccuSpin Micro 17R</td>
			<td>Fisher Scientific</td>
			<td>13-100-675</td>
			<td></td>
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			<td>AlDeSense</td>
			<td></td>
			<td></td>
			<td>Synthesized in-house</td>
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		<tr>
			<td>BG-1</td>
			<td></td>
			<td></td>
			<td>A gift provided by the Prof. Paul Hergenrother Lab, University of Illinois Urbana-Champaign</td>
		</tr>
		<tr>
			<td>BioLite 25cm2 Flask</td>
			<td>Thermo Fisher Scientific&#160;</td>
			<td>130189</td>
			<td></td>
		</tr>
		<tr>
			<td>Biosafety Cabinet 1300 series A2</td>
			<td>Thermo Fisher Scientific&#160;</td>
			<td></td>
			<td></td>
		</tr>
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			<td>Caov-3</td>
			<td></td>
			<td></td>
			<td>A gift provided by the Prof. Erik Nelson Lab, University of Illinois Urbana-Champaign</td>
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			<td>Cell homogenizer</td>
			<td>Fisher Scientific</td>
			<td></td>
			<td></td>
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		<tr>
			<td>Centrifuge 5180R</td>
			<td>Eppendorf</td>
			<td>22627040</td>
			<td></td>
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			<td>Contrl-AlDeSense</td>
			<td></td>
			<td></td>
			<td>Synthesized in-house</td>
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			<td>DMEM, 10% FBS, 1% P/S</td>
			<td></td>
			<td></td>
			<td>Prepared by UIUC cell media facility</td>
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			<td>Falcon Round-Bottom Polystyrene Test Tubes with Cell Strainer Snap Cap, 5mL</td>
			<td>Corning</td>
			<td>352003</td>
			<td></td>
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		<tr>
			<td>FCS Express 6</td>
			<td></td>
			<td></td>
			<td>Provided by UIUC CMtO</td>
		</tr>
		<tr>
			<td>FL microscope</td>
			<td>EVOS</td>
			<td></td>
			<td></td>
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			<td>Fluorometer</td>
			<td>Photon Technology International</td>
			<td></td>
			<td></td>
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			<td>Forma Series II Water-Jacketed CO2&#160;Incubator</td>
			<td>Fisher Scientific</td>
			<td>3110</td>
			<td></td>
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			<td>IGROV-1</td>
			<td></td>
			<td></td>
			<td>A gift provided by the Prof. Erik Nelson Lab, University of Illinois Urbana-Champaign</td>
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			<td>ImageJ</td>
			<td>NIH</td>
			<td></td>
			<td></td>
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			<td>Innova 42R Incubated Shaker</td>
			<td></td>
			<td></td>
			<td></td>
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			<td>LSM 700</td>
			<td>Zeiss</td>
			<td></td>
			<td></td>
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			<td>LSR II</td>
			<td>BD</td>
			<td></td>
			<td></td>
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			<td>Nunc Lab-Tek Chambered #1.0 Borosicilate Coverglass System</td>
			<td>Thermo Fisher Scientific&#160;</td>
			<td>155383</td>
			<td></td>
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		<tr>
			<td>OVCAR-3</td>
			<td>ATCC</td>
			<td>HTB-161</td>
			<td></td>
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			<td>PEO4</td>
			<td></td>
			<td></td>
			<td>A gift provided by the Prof. Erik Nelson Lab, University of Illinois Urbana-Champaign</td>
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		<tr>
			<td>Pierce Protease Inhibitor Tablets</td>
			<td>Thermo Scientific</td>
			<td>A32963</td>
			<td></td>
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			<td>Poly-L-Lysine</td>
			<td>Cultrex</td>
			<td>3438-100-01</td>
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			<td>Rocker</td>
			<td>VWR</td>
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			<td>RPMI, 10% FBS, 1% P/S</td>
			<td></td>
			<td></td>
			<td>Prepared by UIUC cell media facility</td>
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			<td>RPMI, 20% FBS, 1% P/S, 0.01 mg/mL Insulin</td>
			<td></td>
			<td></td>
			<td>Prepared by UIUC cell media facility</td>
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application of aldesense to stratify ovarian cancer cells based on aldehyde dehydrogenase 1a1 activity

Relapse after cancer treatment is often attributed to the persistence of a subpopulation of tumor cells known as cancer stem cells (CSCs), which are characterized by their remarkable tumor-initiating and self-renewal capacity. Depending on the origin of the tumor (e.g., ovaries), the CSC surface biomarker profile can vary dramatically, making the identification of such cells via immunohistochemical staining a challenging endeavor. On the contrary, aldehyde dehydrogenase 1A1 (ALDH1A1) has emerged as an excellent marker to identify CSCs, owing to its conserved expression profile in nearly all progenitor cells including CSCs. The ALDH1A1 isoform belongs to a superfamily of 19 enzymes that are responsible for the oxidation of various endogenous and xenobiotic aldehydes to the corresponding carboxylic acid products. Chan et al. recently developed AlDeSense, an isoform-selective "turn-on" probe for the detection of ALDH1A1 activity, as well as a non-reactive matching control reagent (Ctrl-AlDeSense) to account for off-target staining. This isoform-selective tool has already been demonstrated to be a versatile chemical tool through the detection of ALDH1A1 activity in K562 myelogenous leukemia cells, mammospheres, and melanoma-derived CSC xenografts. In this article, the utility of the probe was showcased through additional fluorimetry, confocal microscopy, and flow cytometry experiments where the relative ALDH1A1 activity was determined in a panel of five ovarian cancer cell lines.

Total ALDH1A1 activity of ovarian cancer cell homogenates 
The average fold turn-ons for each cell line obtained from this assay are: BG-1 (1.12 &#177; 0.01); IGROV-1 (1.30 &#177; 0.03); Caov-3 (1.72 &#177; 0.06); PEO4 (2.51 &#177; 0.29); and OVCAR-3 (10.25 &#177; 1.46) (Figure 2).
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/64713/64713fig02.jpg" /> 
Figure 2<...

Watch this Scientific Journal Video about Application of AlDeSense to Stratify Ovarian Cancer Cells Based on Aldehyde Dehydrogenase 1A1 Activity at JoVE.com

Application of AlDeSense to Stratify Ovarian Cancer Cells Based on Aldehyde Dehydrogenase 1A1 Activity

Methods to measure ALDH1A1 activity in live cells are critical in cancer research due to its status as a biomarker of stemness. In this study, we employed an isoform-selective fluorogenic probe to determine the relative levels of ALDH1A1 activity in a panel of five ovarian cancer cell lines.

Relapse after cancer treatment is often attributed to the persistence of a subpopulation of tumor cells known as cancer stem cells (CSCs), which are ...

application-aldesense-to-stratify-ovarian-cancer-cells-based-on

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Cancer Research

942 Views.  University of Illinois Urbana-Champaign. Methods to measure ALDH1A1 activity in live cells are critical in cancer research due to its status as a biomarker of stemness. In this study, we employed an isoform-selective fluorogenic probe to determine the relative levels of ALDH1A1 activity in a panel of five ovarian cancer cell lines.

Video: Application of AlDeSense to Stratify Ovarian Cancer Cells Based on Aldehyde Dehydrogenase 1A1 Activity

Analysis of Cancer Cell Invasion and Anti-metastatic Drug Screening Using Hydrogel Micro-chamber Array (HMCA)-based Plates

Cancer metastasis is known to cause 90% of cancer lethality. Metastasis is a multistage process which initiates with the penetration/invasion of tumor cells into neighboring tissue. Thus, invasion is a crucial step in metastasis, making the invasion process research and development of anti-metastatic drugs, highly significant. To address this demand, there is a need to develop 3D in vitro models which imitate the architecture of solid tumors and their microenvironment most closely to in vivo state on one hand, but at the same time be reproducible, robust and suitable for high yield and high content measurements. Currently, most invasion assays lean on sophisticated microfluidic technologies which are adequate for research but not for high volume drug screening. Other assays using plate-based devices with isolated individual spheroids in each well are material consuming and have low sample size per condition. The goal of the current protocol is to provide a simple and reproducible biomimetic 3D cell-based system for the analysis of invasion capacity in large populations of tumor spheroids. We developed a 3D model for invasion assay based on HMCA imaging plate for the research of tumor invasion and anti-metastatic drug discovery. This device enables the production of numerous uniform spheroids per well (high sample size per condition) surrounded by ECM components, while continuously and simultaneously observing and measuring the spheroids at single-element resolution for medium throughput screening of anti-metastatic drugs. This platform is presented here by the production of HeLa and MCF7 spheroids for exemplifying single cell and collective invasion. We compare the influence of the ECM component hyaluronic acid (HA) on the invasive capacity of collagen surrounding HeLa spheroids. Finally, we introduce Fisetin (invasion inhibitor) to HeLa spheroids and nitric oxide (NO) (invasion activator) to MCF7 spheroids. The results are analyzed by in-house software which enables semi-automatic, simple and fast analysis which facilitates multi-parameter examination.

Analysis of Cancer Cell Invasion and Anti-metastatic Drug Screening Using Hydrogel Micro-chamber Array HMCA-based Plates

A HMCA-based imaging plate is presented for invasion assay performance. This plate facilitates the formation of three-dimensional (3D) tumor spheroids and the measurement of cancer cell invasion into the extracellular matrix (ECM). The invasion assay quantification is achieved by semi-automatic analysis.

Cancer metastasis is known to cause 90% of cancer lethality. Metastasis is a multistage process which initiates with the penetration/invasion of tumor ...

A Three-dimensional Thymic Culture System to Generate Murine Induced Pluripotent Stem Cell-derived Tumor Antigen-specific Thymic Emigrants

The inheritance of pre-rearranged T cell receptors (TCRs) and their epigenetic rejuvenation make induced pluripotent stem cell (iPSC)-derived T cells a promising source for adoptive T cell therapy (ACT). However, classical in vitro methods for producing regenerated T cells from iPSC result in either innate-like or terminally differentiated T cells, which are phenotypically and functionally distinct from na&#239;ve T cells. Recently, a novel three-dimensional (3D) thymic culture system was developed to generate a homogenous subset of CD8&#945;&#946;+ antigen-specific T cells with a na&#239;ve T cell-like functional phenotype, including the capacity for proliferation, memory formation, and tumor suppression in vivo. This protocol avoids aberrant developmental fates, allowing for the generation of clinically relevant iPSC-derived T cells, designated as iPSC-derived thymic emigrants (iTE), while also providing a potent tool to elucidate the subsequent functions necessary for T cell maturation after thymic selection.

This article describes a novel method to generate tumor antigen-specific induced pluripotent stem cell-derived thymic emigrants (iTE) by a three-dimensional (3D) thymic culture system. iTE are a homogenous subset of T cells closely related to na&#239;ve T cells with the capacity for proliferation, memory formation, and tumor suppression.

The inheritance of pre-rearranged T cell receptors (TCRs) and their epigenetic rejuvenation make induced pluripotent stem cell (iPSC)-derived T cells a ...

Using Human Induced Pluripotent Stem Cells for the Generation of Tumor Antigen-specific T Cells

The generation and expansion of functional T cells in vitro can lead to a broad range of clinical applications. One such use is for the treatment of patients with advanced cancer. Adoptive T cell transfer (ACT) of highly enriched tumor antigen-specific T cells has been shown to cause durable regression of metastatic cancer in some patients. However, during expansion, these cells may become exhausted or senescent, limiting their effector function and persistence in vivo. Induced pluripotent stem cell (iPSC) technology may overcome these obstacles by leading to in vitro generation of large numbers of less differentiated tumor antigen-specific T cells. Human iPSC (hiPSC) have the capacity to differentiate into any type of somatic cell, including lymphocytes, which retain the original T cell receptor (TCR) genomic rearrangement when a T cell is used as a starting cell. Therefore, reprogramming of human tumor antigen-specific T cells to hiPSC followed by redifferentiation to T cell lineage has the potential to produce rejuvenated tumor antigen-specific T cells. Described here is a method for generating tumor antigen-specific CD8&#945;&#946;+ single positive (SP) T cells from hiPSC using OP9/DLL1 co-culture system. This method is a powerful tool for in vitro T cell lineage generation and will facilitate the development of in vitro derived T cells for use in regenerative medicine and cell-based therapies.

This article describes a method to generate functional tumor antigen-specific induced pluripotent stem cell-derived CD8&#945;&#946;+ single positive T cells using OP9/DLL1 co-culture system.

The generation and expansion of functional T cells in vitro can lead to a broad range of clinical applications. One such use is for the treatment of ...

Preparation of Mitochondria from Ovarian Cancer Tissues and Control Ovarian Tissues for Quantitative Proteomics Analysis

Ovarian cancer is a common gynecologic cancer with high mortality but unclear molecular mechanism. Most ovarian cancers are diagnosed in the advanced stage, which seriously hampers therapy. Mitochondrial changes are a hallmark of human ovarian cancers, and mitochondria are the centers of energy metabolism, cell signaling, and oxidative stress. In-depth insights into the changes of the mitochondrial proteome in ovarian cancers compared to control ovarian tissue will benefit in-depth understanding of the molecular mechanisms of ovarian cancer, and the discovery of effective and reliable biomarkers and therapeutic targets. An effective mitochondrial preparation method coupled with an isobaric tag for relative and absolute quantification (iTRAQ) quantitative proteomics are presented here to analyze human ovarian cancer and control mitochondrial proteomes, including differential-speed centrifugation, density gradient centrifugation, quality assessment of mitochondrial samples, protein digestion with trypsin, iTRAQ labeling, strong cation exchange fractionation (SCX), liquid chromatography (LC), tandem mass spectrometry (MS/MS), database analysis, and quantitative analysis of mitochondrial proteins. Many proteins have been successfully identified to maximize the coverage of the human ovarian cancer mitochondrial proteome and to achieve the differentially expressed mitochondrial protein profile in human ovarian cancers.

This article presents a protocol of differential-speed centrifugation in combination with density gradient centrifugation to separate mitochondria from human ovarian cancer tissues and control ovarian tissues for quantitative proteomics analysis, resulting in a high-quality mitochondrial sample and high-throughput and high-reproducibility quantitative proteomics analysis of a human ovarian cancer mitochondrial proteome.

Ovarian cancer is a common gynecologic cancer with high mortality but unclear molecular mechanism. Most ovarian cancers are diagnosed in the advanced ...

Orthotopic Implantation of Patient-Derived Cancer Cells in Mice Recapitulates Advanced Colorectal Cancer

Over the last decade, more sophisticated preclinical colorectal cancer (CRC) models have been established using patient-derived cancer cells and 3D tumoroids. Since patient derived tumor organoids can retain the characteristics of the original tumor, these reliable preclinical models enable cancer drug screening and the study of drug resistance mechanisms. However, CRC related death in patients is mostly associated with the presence of metastatic disease. It is therefore essential to evaluate the efficacy of anti-cancer therapies in relevant in vivo models that truly recapitulate the key molecular features of human cancer metastasis. We have established an orthotopic model based on the injection of CRC patient-derived cancer cells directly into the cecum wall of mice. These tumor cells develop primary tumors in the cecum that metastasize to the liver and lungs, which is frequently observed in patients with advanced CRC. This CRC mouse model can be used to evaluate drug responses monitored by microcomputed tomography (&#181;CT), a clinically relevant small-scale imaging method that can easily identify primary tumors or metastases in patients. Here, we describe the surgical procedure and the required methodology to implant patient-derived cancer cells in the cecum wall of immunodeficient mice.

This protocol describes the orthotopic implantation of patient-derived cancer cells in the cecum wall of immunodeficient mice. The model recapitulates advanced colorectal cancer metastatic disease and allows for the evaluation of new therapeutic drugs in a clinically relevant scenario of lung and liver metastases.

Over the last decade, more sophisticated preclinical colorectal cancer (CRC) models have been established using patient-derived cancer cells and 3D ...

Quantifying Replication Stress in Ovarian Cancer Cells Using Single-Stranded DNA Immunofluorescence

Replication stress is a hallmark of several ovarian cancers. Replication stress can emerge from multiple sources, including double-strand breaks, transcription-replication conflicts, or amplified oncogenes, inevitably resulting in the generation of single-stranded DNA (ssDNA). Quantifying ssDNA, therefore, presents an opportunity to assess the level of replication stress in different cell types and under various DNA-damaging conditions or treatments. Emerging evidence also suggests that ssDNA can be a predictor of responses to chemotherapeutic drugs that target DNA repair. Here, we describe a detailed immunofluorescence-based methodology to quantify ssDNA. This methodology involves labeling the genome with a thymidine analog, followed by the antibody-based detection of the analog at the chromatin under non-denaturing conditions. Stretches of ssDNA can be visualized as foci under a fluorescence microscope. The number and intensity of the foci directly co-relate with the level of ssDNA present in the nucleus. We also describe an automated pipeline to quantify the ssDNA signal. The method is rapid and reproducible. Furthermore, the simplicity of this methodology makes it amenable to high-throughput applications such as drug and genetic screens.

Here, we describe an immunofluorescence-based method to quantify the levels of single-stranded DNA in cells. This efficient and reproducible method can be utilized to examine replication stress, a common feature in several ovarian cancers. Additionally, this assay is compatible with an automated analysis pipeline, which further increases its efficiency.

Replication stress is a hallmark of several ovarian cancers. Replication stress can emerge from multiple sources, including double-strand breaks, ...

Quantifying Telomere Length Using Non-Radioactive Chemiluminescence Detection

Optimization of Performance Parameters of the TAGGG Telomere Length Assay

Telomeres are repetitive sequences which are present at chromosomal ends; their shortening is a characteristic feature of human somatic cells. Shortening occurs due to a problem with end replication and the absence of the telomerase enzyme, which is responsible for maintaining telomere length. Interestingly, telomeres also shorten in response to various internal physiological processes, like oxidative stress and inflammation, which may be impacted due to extracellular agents like pollutants, infectious agents, nutrients, or radiation. Thus, telomere length serves as an excellent biomarker of aging and various physiological health parameters. The TAGGG telomere length assay kit is used to quantify average telomere lengths using the telomere restriction fragment (TRF) assay and is highly reproducible. However, it is an expensive method, and because of this, it is not employed routinely for large sample numbers. Here, we describe a detailed protocol for an optimized and cost-effective measurement of telomere length using Southern blots or TRF analysis and non-radioactive chemiluminescence-based detection.

Author Spotlight: Optimization of Performance Parameters of the TAGGG Telomere Length Assay  

Here, we describe in detail the protocol for quantifying telomere length using non-radioactive chemiluminescent detection, with a focus on the optimization of various performance parameters of the TAGGG telomere length assay kit, such as buffer quantities and probe concentrations.

Telomeres are repetitive sequences which are present at chromosomal ends; their shortening is a characteristic feature of human somatic cells. Shortening ...

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Human Omentum Specimen Processing and Co-Culture with Ovarian Cancer Cells

Standardizing Ovarian Cancer Organoid Biobanking

Strategy for Biobanking of Ovarian Cancer Organoids: Addressing the Interpatient Heterogeneity across Histological Subtypes and Disease Stages

While the establishment of an ovarian cancer biobank from patient-derived organoids along with their clinical background information promises advances in research and patient care, standardization remains a challenge due to the heterogeneity of this lethal malignancy, combined with the inherent complexity of organoid technology. This adaptable protocol provides a systematic framework to realize the full potential of ovarian cancer organoids considering a patient-specific variability of progenitors. By implementing a structured experimental workflow to select optimal culture conditions and seeding methods, with parallel testing of direct 3D seeding versus a 2D/3D route, we obtain, in most cases, robust long-term expanding lines suitable for a broad range of downstream applications. 
Notably, the protocol has been tested and proven efficient in a great number of cases (N = 120) of highly heterogeneous starting material, including high-grade and low-grade ovarian cancer and stages of the disease with primary debulking, recurrent disease, and post-neoadjuvant surgical specimens. Within a low Wnt, high BMP exogenous signaling environment, we observed progenitors being differently susceptible to the activation of the Heregulin 1 &#223; (HER&#223;-1)-pathway, with HER&#223;-1 promoting organoid formation in some while inhibiting it in others. For a subset of the patient's samples, optimal organoid formation and long-term growth necessitate the addition of fibroblast growth factor 10 and R-Spondin 1 to the medium. 
Further, we highlight the critical steps of tissue digestion and progenitor isolation and point to examples where brief cultivation in 2D on plastic is beneficial for subsequent organoid formation in the Basement Membrane Extract type 2 matrix. Overall, optimal biobanking requires systematic testing of all main conditions in parallel to identify an adequate growth environment for individual lines. The protocol also describes the handling procedure for efficient embedding, sectioning, and staining to obtain high-resolution images of organoids, which is required for comprehensive phenotyping.

Author Spotlight: Advancing Personalized Medicine in Ovarian Cancer 

This protocol offers a systematic framework for the establishment of ovarian cancer organoids from different disease stages and addresses the challenges of patient-specific variability to increase yield and enable robust long-term expansion for subsequent applications. It includes detailed steps for tissue processing, seeding, adjusting media requirements, and immunofluorescence staining.

While the establishment of an ovarian cancer biobank from patient-derived organoids along with their clinical background information promises advances in ...