This study was supported by the Leo and Anne Albert Charitable Foundation and JM Foundation. We thank the University of California San Diego Moores Cancer Center members, Dr. Jing Yang and Dr. Kay T. Yeung for allowing us the use of their microtome and Randall French, Department of Surgery for technical expertise.

This study was carried out in strict accordance with the recommendations in the Guide for the University of California San Diego (UCSD) Institutional Review Board (IRB). IRB #090401 Approval was received from the UCSD Institutional Review Board (IRB) to collect surgical specimen from patients for research purposes. An informed consent was obtained from each patient and a surgical bone prostate cancer metastasis specimen was obtained from orthopedic repair of a pathologic fracture in the femur. Animal protocols were performed under the University of California San Diego (UCSD) animal welfare and Institutional Animal Care and Use Committee (IACUC) approved protocol #S10298. Cells from mechanically and enzymatically dissociated patient tumor tissue were intra-femorally injected into 6 to 8 week old male Rag2-/-;&#947;c-/- mice as previously described17. Xenograft tumor volume was determined using an in vivo bioluminescence imaging system and caliper measurements. Upon tumor growth up to 2.0 cm (the maximal allowable size approved by IACUC), the tumor was harvested for 3D organoids establishment.
NOTE: Figure 1 shows the workflow for establishing 3D Organoids and a protocol number for each step of the experimental procedures.
1. Processing of patient derived xenograft (PDX) tumor tissues
NOTE: This is an initial step for organoid establishment for a tumor derived from a xenograft mouse model. This protocol is adapted from a previous publication by Drost et al.5 and we have modified the media conditions to include serum supplementation to organoid media.
<ol>
	<li>Process the tumor specimen as described below.
	<ol>
		<li>Mince tumor samples to 1-3 mm3 sized pieces and digest the samples with 10 mL of cell dissociation solution for 45 min at room temperature.</li>
		<li>To terminate digestion, add 20 mL of DMEM complete media to the samples.</li>
		<li>Filter the suspension through a 70 &#956;m cell strainer. Use a sterile plunger flange to push any leftover tissue on the top of 70 &#956;m cell strainer.</li>
		<li>Centrifuge at 300 x g for 5 min at 4 &#176;C.</li>
		<li>Wash the cell pellet three times with fresh adDMEM complete media. Match the volume of media for wash and resuspension with the volume of media suggested in Table 3. For example, for a 24 well plate culture condition, the volume for the wash should be 500 &#181;L. 
		NOTE: As shown in Table 3, the protocol is applicable to different culture conditions.</li>
		<li>Determine final cell counts using Trypan blue dye and a hemocytometer.</li>
		<li>After obtaining cell counts, re-suspend cell pellet in 80 &#181;L of 2% FBS in PBS per 2 x 106 tumor cells.</li>
		<li>Add 20 &#181;L of Mouse Cell Depletion Cocktail per 2 x 106 tumor cells. Mix well and incubate for 15 min at 2-8 &#176;C.</li>
		<li>Adjust the volume to 500 &#181;L with 2% FBS in PBS buffer per 2 x 106 tumor cells. 
		NOTE: Up to 1 x 107 tumor cells in 2.5 mL of cell suspension can be processed on one LS column.</li>
		<li>Load the LS columns on the magnetic column separator and place a 15 mL conical tube on a rack underneath to collect the flow-through.</li>
		<li>Rinse each column with 3 mL of 2% FBS in PBS buffer. Discard the conical tube with the wash flow-through and replace with a new, sterile 15 mL conical tube.</li>
		<li>Add the cell suspension (up to 2.5 mL of 1 x 107 tumor cells) onto the column. Collect flow-through that will be the enriched with human tumor cells.</li>
		<li>Wash the column twice with 1 mL of 2% FBS in PBS buffer. 
		NOTE: It is important to perform wash steps as soon as the column is empty. Also, try to avoid forming air bubbles.</li>
	</ol>
	</li>
	<li>Aliquot the appropriate volume of cell suspension to a 1.5 mL tube for the desired culture set up (Table 3).</li>
	<li>Centrifuge the 1.5 mL tube at 300 x g and 4 &#176;C for 5 min.</li>
	<li>Carefully remove and discard the supernatant.</li>
</ol>
2. Processing of patient primary tumor tissues
NOTE: This is an initial step for organoid establishment.
<ol>
	<li>Follow all of step 1 except the mouse cell depletion process, which is not necessary for processing of patient primary tumor tissues.</li>
</ol>
3. Forming an attached round dome on the plate
NOTE: This manuscript describes three ways to make a dome from a mixture of the cell pellet and the basement membrane (e.g., Matrigel) as shown in Figure 1 and Figure 2. In Steps 2-4, the cells and the basement membrane should be kept on ice to prevent solidification of the basement membrane.
<ol>
	<li>Resuspend the cell pellet in the appropriate volume of basement membrane (e.g., 40 &#181;L) for a 24 well plate set up (Table 3).</li>
	<li>Pipette up and down gently to ensure that the cells are re-suspended well in the basement membrane.</li>
	<li>Pipette the appropriate volume (Table 3) of the cell-basement membrane mixture (and optional 10 &#181;L of adDMEM complete media) into the center of the pre-warmed tissue culture plate.</li>
	<li>Invert the plate and immediately place the plate upside down in the CO2 cell culture incubator set at 5% CO2, 37 &#176;C for 15 min. This prevents cells from settling and adhering to the plate bottom while allowing the basement membrane to solidify.</li>
	<li>Pipette the appropriate volume (Table 3) of pre-warmed medium containing 10 &#956;M Y-27632 dihydrochloride into each well.</li>
	<li>Place the plate right side up inside the CO2 cell culture incubator (5% CO2, 37 &#176;C).</li>
	<li>Change the media every 3-4 days. After 5-7 days, use culture medium without 10 &#956;M Y-27632 dihydrochloride to maintain the cultures.</li>
</ol>
4. Forming a floating dome from an attached round dome on the plate
<ol>
	<li>After step 3.7, detach the dome using a cell scraper.</li>
</ol>
5. Forming floating beads
NOTE: This protocol is named as floating beads since the mixture of basement membrane, media, and organoids look like beads.
<ol>
	<li>Cut a 2 inch x 4 inch piece of paraffin film.</li>
	<li>Place the paraffin film on the top of the divots of an empty tip-holding rack from a 1000 &#181;L plastic pipette tip box.</li>
	<li>Gently press down on the paraffin film to trace the divots using a gloved index finger but without breaking through the paraffin film.</li>
	<li>Spray the paraffin film with 70% ethanol and turn on the UV lamp in the cell culture hood to sterilize the prepared paraffin film for at least 30 min.</li>
	<li>Prepare a mixture of cells and 20 &#181;L of basement membrane. Seeding density can be 50,000 - 250,000 cells per dome.</li>
	<li>Pipette the mixture of cells processed from step 1 or 2, and 20 &#181;L of basement membrane into the mold of the divot formed in the prepared paraffin film.</li>
	<li>Resuspend the cell pellet in basement membrane and pipette the cell suspension in the prepared paraffin filmed divots.</li>
	<li>Place the solidified beads and paraffin film into a 6-well plate. One well in a 6-well plate can fit up to 5 beads.</li>
	<li>Pipette 3-5 mL of pre-warmed medium containing 10 &#956;M Y-27632 dihydrochloride into each well while gently brushing beads off of the paraffin film. 
	NOTE: As a minimum volume, 3 mL is recommended. For a maximum number of beads (N=5) per well, 5 mL of medium is recommended.</li>
	<li>Place the plate inside a CO2 incubator (5% CO2, 37 &#176;C).</li>
	<li>Change the organoid media every 3-4 days. After 5-7 days, use culture medium without 10 &#956;M Y-27632 dihydrochloride to maintain the cultures.</li>
</ol>
6. In vivo organoids image stitching using microscope8
NOTE: Certain microscopes are unable to reach the outer perimeter of the cell plate (edge wall); therefore, we suggest using the wells close to the perimeter of the cell plate when image stitching.
<ol>
	<li>Place the cell culture plate in an upward position into the plate holder in the Keyence microscope.</li>
	<li>Place the lens on the center of the target dome.</li>
	<li>Set up the automatic stitching process by selecting number of the frames. For examples, 3 x 3 or 5 x 5 can be chosen to generate 9 images or 25 images total.</li>
	<li>Press the capture button to initiate imaging process.</li>
	<li>Open the image viewer software and load a group of images taken by step 4.</li>
	<li>Click Image Stitching to create a high-resolution stitched image. 
	NOTE: Capturing of serial 9 or 25 images can be performed either by manual or automatic set up to focus the cells.</li>
</ol>
7. Organoid processing for histology: the agarose spin down method
NOTE: This protocol is adapted from a previous publication by Vlachogiannis et al.7. We have added a step involving agarose embedding to successfully embed all populations of organoids.
<ol>
	<li>Remove existing media from the well. Be careful not to aspirate the basement membrane domes.</li>
	<li>Add an equal (equal to the volume of media removed from step 1) volume of cell recovery solution and incubate for 60 min at 4 &#176;C.</li>
	<li>Dislodge the basement membrane dome using a pipette and crush the basement membrane dome using a pipet tip. Collect the dissociated dome and cell recovery solution in a 1.5 mL tube.</li>
	<li>Centrifuge at 300 x g and 4 &#176;C for 5 min.</li>
	<li>Remove the supernatant (cell recovery solution). Save all supernatants in separate tubes until the end when the presence of organoids is confirmed in the final pelleting step.</li>
	<li>Add desired volume (Table 3) of cold PBS and gently pipette up and down to mechanically disturb pellet.</li>
	<li>Centrifuge at 300 x g and 4 &#176;C for 5 min.</li>
	<li>Remove the supernatant (PBS).</li>
	<li>Fix the pellet in a matched volume (e.g., 500 &#181;L for one pellet from the 24 well plate culture condition, Table 3) of 4% PFA for 60 min at room temperature.</li>
	<li>Following fixation, centrifuge at 300 x g and 4 &#176;C for 5 min.</li>
	<li>Remove the supernatant (PFA).</li>
	<li>Wash with matched volume (e.g., 500 &#181;L for one pellet from the 24 well plate culture condition, Table 3) of PBS and centrifuge at 300 x g and 4 &#176;C for 5 min.</li>
	<li>Prepare warm agarose (2% agarose in PBS). 
	NOTE: Here, cell pellets for frozen sections can be directly re-suspended in 200 &#181;L of OCT compound without further steps in Protocol 7.</li>
	<li>Re-suspend the cell pellet in 200 &#181;L of agarose (2% in PBS).
	<ol>
		<li>Immediately after adding agarose, gently detach the cell pellet from the wall of the 1.5 mL tube using the 25 G needle attached to 1 mL syringe. As shown in Figure 3, if the cell pellet is not physically detached from the wall of the 1.5 mL tube, then there is a risk of losing all or part of the cell pellet during the agarose embedding process.</li>
	</ol>
	</li>
	<li>Wait until the 2% agarose in PBS is completely solidified.</li>
	<li>Detach the solidified agarose block from the 1.5 mL tube using a 25 G needle attached to the 1 mL syringe.</li>
	<li>Transfer the detached agarose block containing the cell pellet to a new 1.5 mL tube.</li>
	<li>Fill the tube with 70% EtOH and proceed further using the conventional protocol for tissue dehydration and paraffin embedding.</li>
</ol>
8. Histology and Immunofluorescent cytochemistry (IFC) of organoids
<ol>
	<li>Select the slide(s) for histology or IFC.</li>
	<li>Before initiating the staining process, find out where the cells are located on the slide and draw a circle around the cells on the slide using a marker.</li>
	<li>Draw the perimeter around the edge or boarder of the slide and where circles are located on the slide in a laboratory notebook to record their locations.</li>
	<li>Perform desired staining. 
	NOTE: During this process, marked circles disappear since regular maker is not resistant to the chemicals. Even some histology permanent markers may be erased during staining process.</li>
	<li>After the staining process, place the slide over the drawing in the laboratory notebook to find the locations of cells on the slide.</li>
</ol>

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Sanghee Lee and Christina A.M. Jamieson are the guest editors of JoVE Methods Collection.

3D organoids derived from patient bone metastasis prostate cancer cells are still relatively rare. Here, we describe strategies and further optimized protocol to successfully established serial 3D patient derived organoids (PDOs) of BMPC. In addition, protocols are described to secure the organoids in samples with lower cell density for IFC and IHC analysis. Differential phenotypes in the form of cyst, spheroids and more complex organoids indicate that this protocol provides culture conditions that allows for heterogonou...

Three-dimensional cultured organoids have drawn attention for their potential to recapitulate the in vivo architecture, cellular functionality and genetic signature of their original tissues1,2,3,4,5. Most importantly, 3D organoids established from patient tumor tissues or patient derived xenograft (PDX) models provide invaluable opportunities to understand mechanisms of cellular signaling upon tumorigenesis and to determine the effects of drug treatment on each cell population6,7,8,9,10,11,12,13. Drost et al.5 developed a standard protocol for establishment of human and mouse prostate organoids, which has been widely adopted in the field of urology. In addition, significant effort has been dedicated for further characterization of 3D organoids and to understand the detailed mechanisms of tumorigenesis and metastasis4,12,14,15. In addition to the previously established and widely accepted protocol for 3D organoids cultures, we describe here a step-by-step protocol for the 3D culture of PDO using three different doming methods in optimized culture conditions.
In this manuscript, 3D organoids were established as an ex vivo model of bone metastatic prostate cancer (BMPC). The cells used for these cultures came from the Prostate Cancer San Diego (PCSD) series and were derived directly from patient prostate cancer bone metastatic tumor tissues (PCSD18 and PCSD22) or patient derived xenograft (PDX) tumor models (samples named PCSD1, PCSD13, and PCSD17). Because spontaneous bone metastasis of prostate cancer cells is rare in genetically engineered mouse models16, we used direct intra-femoral (IF) injection of human tumor cells into male Rag2-/-&#947;c-/- mice to establish the PDX models of bone metastatic prostate cancer17.
Once 3D organoids are established from heterogeneous patient tumor cells or patient derived xenografts, it is essential to confirm their identity as prostate tumor cells and to determine their phenotypes in the 3D organoid cultures. Immunofluorescence chemistry (IFC) allows the visualization of protein expression in situ in each cell, often indicating the potential functions for specific cell populations2,4. In general, IFC protocols for a vast majority of samples including tissues and cells are straightforward and fully optimized. However, the cell density and number of organoids can be significantly lower than that of conventional culture. Therefore, the IFC protocol for organoids requires additional steps to ensure proper processing and embedding in paraffin for all organoids in the samples. We describe additional steps for an agarose pre-embedding process and tips to label the location of sectioned organoids on the slide that increases the success rate of IFC on organoids especially when the samples of organoids have lower cell density than desired.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1 mL Pipettman</td>
			<td>Gilson</td>
			<td>F123602</td>
			<td></td>
		</tr>
		<tr>
			<td>1 mL Syringe</td>
			<td>BD Syringe</td>
			<td>329654</td>
			<td></td>
		</tr>
		<tr>
			<td>1.5 mL tube</td>
			<td>Spectrum Lab Products</td>
			<td>941-11326-ATP083</td>
			<td></td>
		</tr>
		<tr>
			<td>25G Needle</td>
			<td>BD PrecisionGlide Needle</td>
			<td>305122</td>
			<td></td>
		</tr>
		<tr>
			<td>4% Paraformaldehyde (PFA)</td>
			<td>Alfa Aesar</td>
			<td>J61899</td>
			<td></td>
		</tr>
		<tr>
			<td>70% Ethanol (EtOH)</td>
			<td>VWR</td>
			<td>BDH1164-4LP</td>
			<td></td>
		</tr>
		<tr>
			<td>A83-01</td>
			<td>Tocris Bioscience</td>
			<td>2939</td>
			<td></td>
		</tr>
		<tr>
			<td>Accumax</td>
			<td>Innovative Cell Technologies, Inc.</td>
			<td>AM105</td>
			<td></td>
		</tr>
		<tr>
			<td>adDMEM</td>
			<td>Life Technologies</td>
			<td>12634010</td>
			<td></td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>Lonza</td>
			<td>50000</td>
			<td></td>
		</tr>
		<tr>
			<td>Antibody -for Cytokeratin 5</td>
			<td>Biolegend</td>
			<td>905901</td>
			<td></td>
		</tr>
		<tr>
			<td>Antibody for Cytokeratin 8</td>
			<td>Biolegend</td>
			<td>904801</td>
			<td></td>
		</tr>
		<tr>
			<td>B27</td>
			<td>Life Technologies</td>
			<td>17504044</td>
			<td></td>
		</tr>
		<tr>
			<td>Bioluminescence imaging system, IVIS 200</td>
			<td>Perkin Elmer Inc</td>
			<td>IVIS 200</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell Culture Plate - 24 well</td>
			<td>Costar</td>
			<td>3524</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell Culture Plate - 48 well</td>
			<td>Costar</td>
			<td>3548</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell Culture Plate - 6 well</td>
			<td>Costar</td>
			<td>3516</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell Dissociation Solution, Accumax</td>
			<td>Innovative Cell Technologies, Inc.</td>
			<td>AM105</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell Recovery Solution</td>
			<td>Corning</td>
			<td>354253</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell Scraper</td>
			<td>Sarstedt</td>
			<td>83.180</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell Strainer</td>
			<td>Falcon (Corning)</td>
			<td>352350</td>
			<td></td>
		</tr>
		<tr>
			<td>CO2 incubator</td>
			<td>Fisher Scientific</td>
			<td>3546</td>
			<td></td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>Vector Vectashield</td>
			<td>H-1200</td>
			<td></td>
		</tr>
		<tr>
			<td>DHT</td>
			<td>Sigma-Aldrich</td>
			<td>D-073-1ML</td>
			<td></td>
		</tr>
		<tr>
			<td>dPBS</td>
			<td>Corning/Cellgro</td>
			<td>21-031-CV</td>
			<td></td>
		</tr>
		<tr>
			<td>EGF</td>
			<td>PeproTech</td>
			<td>AF-100-15</td>
			<td></td>
		</tr>
		<tr>
			<td>FBS</td>
			<td>Gemini Bio-Products</td>
			<td>100-106</td>
			<td></td>
		</tr>
		<tr>
			<td>FGF10</td>
			<td>PeproTech</td>
			<td>100-26</td>
			<td></td>
		</tr>
		<tr>
			<td>FGF2</td>
			<td>PeproTech</td>
			<td>100-18B</td>
			<td></td>
		</tr>
		<tr>
			<td>Forceps</td>
			<td>Denville Scientific</td>
			<td>S728696</td>
			<td></td>
		</tr>
		<tr>
			<td>Glutamax</td>
			<td>Gibco</td>
			<td>35050-061</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Gibco</td>
			<td>15630-080</td>
			<td></td>
		</tr>
		<tr>
			<td>LS Columns</td>
			<td>Miltenyi</td>
			<td>130-0420401</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnetic Column Seperator: QuadroMACS Separator</td>
			<td>Miltenyi</td>
			<td>130-090-976</td>
			<td></td>
		</tr>
		<tr>
			<td>Marker</td>
			<td>VWR</td>
			<td>52877-355</td>
			<td></td>
		</tr>
		<tr>
			<td>Matrigel (Growth Factor Reduced)</td>
			<td>Mediatech Inc. (Corning)</td>
			<td>356231</td>
			<td></td>
		</tr>
		<tr>
			<td>Matrigel (High Concentration)</td>
			<td>BD (Fisher Scientific)</td>
			<td>CB354248</td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope Imaging Software, Keyence</td>
			<td>BZ-X800 (newest software) BZ-X700 (old software)</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope, Keyence</td>
			<td>BZ-X700 (model 2016-2017)/BZ-X710 (model 2018-2019)</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Mouse Cell Depletion Kit</td>
			<td>Miltenyi</td>
			<td>130-104-694</td>
			<td></td>
		</tr>
		<tr>
			<td>N-Acetylcysteine</td>
			<td>Sigma-Aldrich</td>
			<td>A9165-5G</td>
			<td></td>
		</tr>
		<tr>
			<td>Nicotinamide</td>
			<td>Sigma-Aldrich</td>
			<td>N0636-100G</td>
			<td></td>
		</tr>
		<tr>
			<td>Noggin</td>
			<td>PeproTech</td>
			<td>120-10C</td>
			<td></td>
		</tr>
		<tr>
			<td>OCT Compound</td>
			<td>Tissue-Tek</td>
			<td>4583</td>
			<td></td>
		</tr>
		<tr>
			<td>Parafilm</td>
			<td>American National Can</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Pen-Strep</td>
			<td>Mediatech Inc. (Corning)</td>
			<td>30-002-CI-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette tipes for 1 mL (Blue Tips)</td>
			<td>Fisherbrand Redi-Tip</td>
			<td>21-197-85</td>
			<td></td>
		</tr>
		<tr>
			<td>Plunger (from 3 mL syringe)</td>
			<td>BD Syringe</td>
			<td>309657</td>
			<td></td>
		</tr>
		<tr>
			<td>Prostaglandin E2</td>
			<td>Tocris Bioscience</td>
			<td>2296</td>
			<td></td>
		</tr>
		<tr>
			<td>R-Spondin 1</td>
			<td>Trevigen</td>
			<td>3710-001-01</td>
			<td></td>
		</tr>
		<tr>
			<td>SB2021190</td>
			<td>Sigma-Aldrich</td>
			<td>S7076-25MG</td>
			<td></td>
		</tr>
		<tr>
			<td>Small Table Top Centrifuge</td>
			<td>ThermoFisher Scientific</td>
			<td>75002426</td>
			<td></td>
		</tr>
		<tr>
			<td>Water Bath</td>
			<td>Fisher Sci</td>
			<td>2320</td>
			<td></td>
		</tr>
		<tr>
			<td>Y-27632 Dihydrochloride</td>
			<td>Abmole Bioscience</td>
			<td>M1817</td>
			<td></td>
		</tr>
	</tbody>
</table>

establishment and analysis of three-dimensional (3d) organoids derived from patient prostate cancer bone metastasis specimens and their xenografts

Three-dimensional (3D) culture of organoids from tumor specimens of human patients and patient-derived xenograft (PDX) models of prostate cancer, referred to as patient-derived organoids (PDO), are an invaluable resource for studying the mechanism of tumorigenesis and metastasis of prostate cancer. Their main advantage is that they maintain the distinctive genomic and functional heterogeneity of the original tissue compared to conventional cell lines that do not. Furthermore, 3D cultures of PDO can be used to predict the effects of drug treatment on individual patients and are a step towards personalized medicine. Despite these advantages, few groups routinely use this method in part because of the extensive optimization of PDO culture conditions that may be required for different patient samples. We previously demonstrated that our prostate cancer bone metastasis PDX model, PCSD1, recapitulated the resistance of the donor patient&rsquo;s bone metastasis to anti-androgen therapy. We used PCSD1 3D organoids to characterize further the mechanisms of anti-androgen resistance. Following an overview of currently published studies of PDX and PDO models, we describe a step-by-step protocol for 3D culture of PDO using domed or floating basement membrane (e.g., Matrigel) spheres in optimized culture conditions. In vivo stitch imaging and cell processing for histology are also described. This protocol can be further optimized for other applications including western blot, co-culture, etc. and can be used to explore characteristics of 3D cultured PDO pertaining to drug resistance, tumorigenesis, metastasis and therapeutics.

3D organoids were successfully established from a patient derived xenograft (PDX) model of bone metastatic prostate cancer (BMPC) as well as directly from patient bone metastatic prostate cancer tissue (Figure 4). Briefly, our PDX models of BMPC were established by intra-femoral (IF) injection of tumor cells into male Rag2-/- c-/- mice and then PDX tumors were harvested and processed as described in this manuscript. As shown in Figure 4, PD...

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Establishment and Analysis of Three-Dimensional 3D Organoids Derived from Patient Prostate Cancer Bone Metastasis Specimens and their Xenografts

Three-dimensional cultures of patient BMPC specimens and xenografts of bone metastatic prostate cancer maintain the functional heterogeneity of their original tumors resulting in cysts, spheroids and complex, tumor-like organoids. This manuscript provides an optimization strategy and protocol for 3D culture of heterogeneous patient derived samples and their analysis using IFC.

Establishment and Analysis of Three-Dimensional (3D) Organoids Derived from Patient Prostate Cancer Bone Metastasis Specimens and their Xenografts

Three-dimensional (3D) culture of organoids from tumor specimens of human patients and patient-derived xenograft (PDX) models of prostate cancer, referred ...

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9.2K Views.  University of California, San Diego. Three-dimensional cultures of patient BMPC specimens and xenografts of bone metastatic prostate cancer maintain the functional heterogeneity of their original tumors resulting in cysts, spheroids and complex, tumor-like organoids. This manuscript provides an optimization strategy and protocol for 3D culture of heterogeneous patient derived samples and their analysis using IFC.

Video: Establishment and Analysis of Three-Dimensional 3D Organoids Derived from Patient Prostate Cancer Bone Metastasis Specimens and their Xenografts

Labeling of Breast Cancer Patient-derived Xenografts with Traceable Reporters for Tumor Growth and Metastasis Studies

The use of preclinical models to study tumor biology and response to treatment is central to cancer research. Long-established human cell lines, and many transgenic mouse models, often fail to recapitulate the key aspects of human malignancies. Thus, alternative models that better represent the heterogeneity of patients' tumors and their metastases are being developed. Patient-derived xenograft (PDX) models in which surgically resected tumor samples are engrafted into immunocompromised mice have become an attractive alternative as they can be transplanted through multiple generations,and more efficiently reflect tumor heterogeneity than xenografts derived from human cancer cell lines. A limitation to the use of PDXs is that they are difficult to transfect or transduce to introduce traceable reporters or to manipulate gene expression. The current protocol describes methods to transduce dissociated tumor cells from PDXs with high transduction efficiency, and the use of labeled PDXs for experimental models of breast cancer metastases. The protocol also demonstrates the use of labeled PDXs in experimental metastasis models to study the organ-colonization process of the metastatic cascade. Metastases to different organs can be easily visualized and quantified using bioluminescent imaging in live animals, or GFP expression during dissection and in excised organs. These methods provide a powerful tool to extend the use of multiple types of PDXs to metastasis research.

We describe a method for stable labeling of patient-derived xenografts (PDXs) with lentiviral particles expressing green-fluorescent protein and luciferase reporters. This method allows for tracking the growth of PDXs at the primary site, as well as detecting spontaneous and experimental metastases using in vivo imaging systems.

The use of preclinical models to study tumor biology and response to treatment is central to cancer research. Long-established human cell lines, and many ...

Establishment of a Primary Culture of Patient-derived Soft Tissue Sarcoma

Soft tissue sarcomas (STS) represent a spectrum of heterogeneous malignancies with a difficult diagnosis, classification, and management. To date, more than 50 histological subtypes of these rare solid tumors have been identified. Thus, due to their extraordinary diversity and low incidence, our understanding of the biology of these tumors is still limited. Patient-derived cultures represent the ideal platform to study STS pathophysiology and pharmacology. We thus developed a human preclinical model of STS starting from tumor specimens harvested from patients undergoing surgical resection. Patient-derived STS cell cultures were obtained from the surgical specimens by collagenase digestion and isolated by filtration. Cells were counted, seeded, and left for 14 days in standard monolayer cultures and then processed by downstream analysis. Before performing molecular or pharmaceutical analyses, the establishment of STS primary cultures was confirmed through the evaluation of cytomorphologic features and, when available, immunohistochemical markers. This method represents a useful tool 1) to study the natural history of these poorly explored malignancies and 2) to test the effects of different drugs in an effort to learn more about their mechanisms of action.

The following protocol focuses on the establishment of a primary culture of patient-derived soft tissue sarcoma (STS). This model could help us to better understand the molecular background and pharmacological profile of these rare malignancies and could represent a starting point for further research aimed at improving STS management.

Soft tissue sarcomas (STS) represent a spectrum of heterogeneous malignancies with a difficult diagnosis, classification, and management. To date, more ...

Isolation and Characterization of Tumor-initiating Cells from Sarcoma Patient-derived Xenografts

The existence and importance of tumor-initiating cells (TICs) have been supported by increasing evidence during the past decade. These TICs have been shown to be responsible for tumor initiation, metastasis, and drug resistance. Therefore, it is important to develop specific TIC-targeting therapy in addition to current chemotherapy strategies, which mostly focus on the bulk of non-TICs. In order to further understand the mechanism behind the malignancy of TICs, we describe a method to isolate and to characterize TICs in human sarcomas. Herein, we show a detailed protocol to generate patient-derived xenografts (PDXs) of human sarcomas and to isolate TICs by fluorescence-activated cell sorting (FACS) using human leukocyte antigen class I (HLA-1) as a negative marker. Also, we describe how to functionally characterize these TICs, including a sphere formation assay and a tumor formation assay, and to induce differentiation along mesenchymal pathways. The isolation and characterization of PDX TICs provide clues for the discovery of potential targeting therapy reagents. Moreover, increasing evidence suggests that this protocol may be further extended to isolate and characterize TICs from other types of human cancers.

We describe a detailed protocol for the isolation of tumor-initiating cells from human sarcoma patient-derived xenografts by fluorescence-activated cell sorting, using human leukocyte antigen-1 (HLA-1) as a negative marker, and for the further validation and characterization of these HLA-1-negative tumor-initiating cells.

The existence and importance of tumor-initiating cells (TICs) have been supported by increasing evidence during the past decade. These TICs have been ...

Three-Dimensional Bone Extracellular Matrix Model for Osteosarcoma

Osteosarcoma (OS) is the most common and a highly aggressive primary bone tumor. It is characterized with anatomic and histologic variations along with diagnostic or prognostic difficulties. OS comprises genotypically and phenotypically heterogeneous cancer cells. Bone microenvironment elements are proved to account for tumor heterogeneity and disease progression. Bone extracellular matrix (BEM) retains the microstructural matrices and biochemical components of native extracellular matrix. This tissue-specific niche provides a favorable and long-term scaffold for OS cell seeding and proliferation. This article provides a protocol for the preparation of BEM model and its further experimental application. OS cells can grow and differentiate into multiple phenotypes consistent with the histopathological complexity of OS clinical specimens. The model also allows visualization of diverse morphologies and their association with genetic alterations and underlying regulatory mechanisms. As homologous to human OS, this BEM-OS model can be developed and applied to the pathology and clinical research of OS.

The bone extracellular matrix (BEM) model for osteosarcoma (OS) is well established and shown here. It can be used as a suitable scaffold for mimicking primary tumor growth in vitro and providing an ideal model for studying the histologic and cytogenic heterogeneity of OS.

Osteosarcoma (OS) is the most common and a highly aggressive primary bone tumor. It is characterized with anatomic and histologic variations along with ...

Establishment of Gastric Cancer Patient-derived Xenograft Models and Primary Cell Lines

The use of preclinical models to advance our understanding of tumor biology and investigate the efficacy of therapeutic agents is key to cancer research. Although there are many established gastric cancer cell lines and many conventional transgenic mouse models for preclinical research, the disadvantages of these in vitro and in vivo models limit their applications. Because the characteristics of these models have changed in culture, they no longer model tumor heterogeneity, and their responses have not been able to predict responses in humans. Thus, alternative models that better represent tumor heterogeneity are being developed. Patient-derived xenograft (PDX) models preserve the histologic appearance of cancer cells, retain intratumoral heterogeneity, and better reflect the relevant human components of the tumor microenvironment. However, it usually takes 4-8 months to develop a PDX model, which is longer than the expected survival of many gastric patients. For this reason, establishing primary cancer cell lines may be an effective complementary method for drug response studies. The current protocol describes methods to establish PDX models and primary cancer cell lines from surgical gastric cancer samples. These methods provide a useful tool for drug development and cancer biology research.

The current protocol describes methods to establish patient-derived xenograft (PDX) models and primary cancer cell lines from surgical gastric cancer samples. The methods provide a useful tool for drug development and cancer biology research.

The use of preclinical models to advance our understanding of tumor biology and investigate the efficacy of therapeutic agents is key to cancer research. ...

Testing Targeted Therapies in Cancer using Structural DNA Alteration Analysis and Patient-Derived Xenografts

We present here an integrative approach for testing efficacy of targeted therapies that combines the next generation sequencing technolo-gies, therapeutic target analyses and drug response monitoring using patient derived xenografts (PDX). This strategy was validated using ovarian tumors as an example. The mate-pair next generation sequencing (MPseq) protocol was used to identify structural alterations and followed by analysis of potentially targetable alterations. Human tumors grown in immunocompromised mice were treated with drugs selected based on the genomic analyses. Results demonstrated a good correlation between the predicted and the observed responses in the PDX model. The presented approach can be used to test the efficacy of combination treatments and aid personalized treatment for patients with recurrent cancer, specifically in cases when standard therapy fails and there is a need to use drugs off label.

Here we present a protocol to test the efficacy of targeted therapies selected based on the genomic makeup of a tumor. The protocol describes identification and validation of structural DNA rearrangements, engraftment of patients&#8217; tumors into mice and testing responses to corresponding drugs.

We present here an integrative approach for testing efficacy of targeted therapies that combines the next generation sequencing technolo-gies, therapeutic ...

Enhanced Viability for Ex vivo 3D Hydrogel Cultures of Patient-Derived Xenografts in a Perfused Microfluidic Platform

Patient-derived xenografts (PDX), generated when resected patient tumor tissue is engrafted directly into immunocompromised mice, remain biologically stable, thereby preserving molecular, genetic, and histological features, as well as heterogeneity of the original tumor. However, using these models to perform a multitude of experiments, including drug screening, is prohibitive both in terms of cost and time. Three-dimensional (3D) culture systems are widely viewed as platforms in which cancer cells retain their biological integrity through biochemical interactions, morphology, and architecture. Our team has extensive experience culturing PDX cells in vitro using 3D matrices composed of hyaluronic acid (HA). In order to separate mouse fibroblast stromal cells associated with PDXs, we use rotation culture, where stromal cells adhere to the surface of tissue culture-treated plates while dissociated PDX tumor cells float and self-associate into multicellular clusters. Also floating in the supernatant are single, often dead cells, which present a challenge in collecting viable PDX clusters for downstream encapsulation into hydrogels for 3D cell culture. In order to separate these single cells from live cell clusters, we have employed density step gradient centrifugation. The protocol described here allows for the depletion of non-viable single cells from the healthy population of cell clusters that will be used for further in vitro experimentation. In our studies, we incorporate the 3D cultures in microfluidic plates which allow for media perfusion during culture. After assessing the resultant cultures using a fluorescent image-based viability assay of purified versus non-purified cells, our results show that this additional separation step substantially reduced the number of non-viable cells from our cultures.

This protocol demonstrates methods to enable extended in vitro culture of patient-derived xenografts (PDX). One step enhances overall viability of multicellular cluster cultures in 3D hydrogels, through straightforward removal of non-viable single cells. A secondary step demonstrates best practices for PDX culture in a perfused microfluidic platform.

Patient-derived xenografts (PDX), generated when resected patient tumor tissue is engrafted directly into immunocompromised mice, remain biologically ...

Drug Screening of Primary Patient Derived Tumor Xenografts in Zebrafish

Patient derived xenograft models are critical in defining how different cancers respond to drug treatment in an in vivo system. Mouse models are the standard in the field, but zebrafish have emerged as an alternative model with several advantages, including the ability for high-throughput and low-cost drug screening. Zebrafish also allow for in vivo drug screening with large replicate numbers that were previously only obtainable with in vitro systems. The ability to rapidly perform large scale drug screens may open up the possibility for personalized medicine with rapid translation of results back to clinic. Zebrafish xenograft models could also be used to rapidly screen for actionable mutations based on tumor response to targeted therapies or to identify new anti-cancer compounds from large libraries. The current major limitation in the field has been quantifying and automating the process so that drug screens can be done on a larger scale and be less labor-intensive. We have developed a workflow for xenografting primary patient samples into zebrafish larvae and performing large scale drug screens using a fluorescence microscope equipped imaging unit and automated sampler unit. This method allows for standardization and quantification of engrafted tumor area and response to drug treatment across large numbers of zebrafish larvae. Overall, this method is advantageous over traditional cell culture drug screening as it allows for growth of tumor cells in an in vivo environment throughout drug treatment, and is more practical and cost-effective than mice for large scale in vivo drug screens.

Zebrafish xenograft models allow for high-throughput drug screening and fluorescent imaging of human cancer cells in an in vivo microenvironment. We developed a workflow for large scale, automated drug screening on patient-derived leukemia samples in zebrafish using an automated fluorescence microscope equipped imaging unit.

Patient derived xenograft models are critical in defining how different cancers respond to drug treatment in an in vivo system. Mouse models are the ...

The Establishment and Utilization of Patient Derived Xenograft Models of Central Nervous System Metastasis

The development of novel therapies for central nervous system (CNS) metastasis has been hindered by the lack of preclinical models that accurately represent the disease. Patient derived xenograft (PDX) models of CNS metastasis have been shown to better represent the phenotypic and molecular characteristics of the human disease, as well as better reflect the heterogeneity and clonal dynamics of human patient tumors compared to historic cell line models. There are multiple sites that can be used to implant patient-derived tissue when setting up preclinical trials, each with their own advantages and disadvantages, and each suited for studying different aspects of the metastatic cascade. Here, the protocol describes how to establish PDX models and present three different approaches for utilizing CNS metastasis PDX models in pre-clinical studies, discussing each of their applications and limitations. These include flank implantation, orthotopic injection in the brain, and intracardiac injection. Subcutaneous flank implantation is the easiest to monitor and, therefore, most convenient for pre-clinical studies. In addition, metastases to brain and other tissues from flank implantation were observed, indicating that the tumor has undergone multiple steps of metastasis, including intravasation, extravasation, and colonization. Orthotopic injection in the brain is the best option for recapitulating the brain tumor microenvironment and is useful for determining the efficacy of biologics to cross the blood-brain barrier (BBB) but bypasses most steps of the metastatic cascade. Intracardiac injection facilitates metastasis to the brain and is also useful for studying organ tropism. While this method forgoes earlier steps of the metastatic cascade, these cells will still have to survive circulation, extravasate, and colonize. The utility of a PDX model, is therefore, impacted by the route of tumor inoculation and the choice of which one to utilize should be dictated by the scientific question and overall goals of the experiment.

Central nervous system metastasis PDX models represent the phenotypic and molecular characteristics of human metastasis, making them excellent models for preclinical studies. Described here is how to establish PDX models and the inoculation routes that are best used for preclinical studies.

The development of novel therapies for central nervous system (CNS) metastasis has been hindered by the lack of preclinical models that accurately ...

Establishing 3-Dimensional Spheroids from Patient-Derived Tumor Samples and Evaluating their Sensitivity to Drugs

Despite remarkable advances in understanding tumor biology, the vast majority of oncology drug candidates entering clinical trials fail, often due to a lack of clinical efficacy. This high failure rate illuminates the inability of the current preclinical models to predict clinical efficacy, mainly due to their inadequacy in reflecting tumor heterogeneity and the tumor microenvironment. These limitations can be addressed with 3-dimensional (3D) culture models (spheroids) established from human tumor samples derived from individual patients. These 3D cultures represent real-world biology better than established cell lines that do not reflect tumor heterogeneity. Furthermore, 3D cultures are better than 2-dimensional (2D) culture models (monolayer structures) since they replicate elements of the tumor environment, such as hypoxia, necrosis, and cell adhesion, and preserve the natural cell shape and growth. In the present study, a method was developed for preparing primary cultures of cancer cells from individual patients that are 3D and grow in multicellular spheroids. The cells can be derived directly from patient tumors or patient-derived xenografts. The method is widely applicable to solid tumors (e.g., colon, breast, and lung) and is also cost-effective, as it can be performed in its entirety in a typical cancer research/cell biology lab without relying on specialized equipment. Herein, a protocol is presented for generating 3D tumor culture models (multicellular spheroids) from primary cancer cells and evaluating their sensitivity to drugs using two complementary approaches: a cell-viability assay (MTT) and microscopic examinations. These multicellular spheroids can be used to assess potential drug candidates, identify potential biomarkers or therapeutic targets, and investigate the mechanisms of response and resistance.

The present protocol describes generating 3D tumor culture models from primary cancer cells and evaluating their sensitivity to drugs using cell-viability assays and microscopic examinations.

Despite remarkable advances in understanding tumor biology, the vast majority of oncology drug candidates entering clinical trials fail, often due to a ...