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Method Article

Prostate Organoid Cultures as Tools to Translate Genotypes and Mutational Profiles to Pharmacological Responses

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DOI:

10.3791/60346

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October 24th, 2019

 ,  ,  , 
1Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 2Howard Hughes Medical Institute

In This Article

Summary

Presented here is a protocol to study pharmacological responses in prostate epithelial organoids. Organoids closely resemble in vivo biology and recapitulate patient genetics, making them attractive model systems. Prostate organoids can be established from wildtype prostates, genetically engineered mouse models, benign human tissue, and advanced prostate cancer.

Abstract

Presented here is a protocol to study pharmacodynamics, stem cell potential, and cancer differentiation in prostate epithelial organoids. Prostate organoids are androgen responsive, three-dimensional (3D) cultures grown in a defined medium that resembles the prostatic epithelium. Prostate organoids can be established from wild-type and genetically engineered mouse models, benign human tissue, and advanced prostate cancer. Importantly, patient derived organoids closely resemble tumors in genetics and in vivo tumor biology. Moreover, organoids can be genetically manipulated using CRISPR/Cas9 and shRNA systems. These controlled genetics make the organoid culture attractive as a platform for rapidly testing the effects of genotypes and mutational profiles on pharmacological responses. However, experimental protocols must be specifically adapted to the 3D nature of organoid cultures to obtain reproducible results. Described here are detailed protocols for performing seeding assays to determine organoid formation capacity. Subsequently, this report shows how to perform drug treatments and analyze pharmacological response via viability measurements, protein isolation, and RNA isolation. Finally, the protocol describes how to prepare organoids for xenografting and subsequent in vivo growth assays using subcutaneous grafting. These protocols yield highly reproducible data and are widely applicable to 3D culture systems.

Introduction

Drug resistance is one of the major clinical problems in cancer treatment. Metastatic prostate cancer (PCa) treatment is primarily directed at the androgen-signaling axis. Next-generation anti-androgen therapies (e.g., enzalutamide and abiraterone) have showed great clinical success, but virtually all PCa eventually progresses towards an androgen-independent state, or castration resistant prostate cancer (CRPC).

Recent genomic and transcriptomic profiling of CRPC revealed there are three general mechanisms of resistance in prostate cancer: 1) activating mutations resulting in the restoration of androgen receptor (AR) signaling1; 2) activation of bypass signaling, as exemplified in a pre-clinical model for next-generation anti-androgen therapy resistance in which activation of the glucocorticoid receptor (GR) can compensate for loss of AR signaling2; and 3) the recently identified process of lineage plasticity, in which tumor cells acquire resistance by switching lineages from a cell type dependent on the drug target to another cell type that is not dependent on this (which, in PCa, is represented as AR-negative and/or neuroendocrine disease [NEPC])3,4. However, the molecular mechanisms that cause drug resistance are not understood. Moreover, acquired anti-androgen resistance may lead to therapeutic vulnerabilities that can be exploited. Therefore, it is essential to evaluate drug responses in model systems that mimic patient phenotypes and genotypes.

Prostate organoids are organotypic cultures grown in a 3D protein matrix with a defined medium. Importantly, prostate organoids can be established from benign and cancerous tissue of murine or human origin, and they retain phenotypic and genotypic features found in vivo5,6. Importantly, both anti-androgen sensitive PCa and CRPC cells are represented in the current compendium of organoids. Moreover, prostate organoids are easily genetically manipulated using CRISPR/Cas9 and shRNA5. Thus, prostate organoids are a suitable model system for testing drug responses and elucidating resistance mechanisms. Here, a detailed protocol is described to perform drug testing and analyze pharmacological responses using prostate organoids.

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Protocol

All work described in this protocol has been performed with previously established murine organoids and patient-derived organoids. All animal work was performed in compliance with the guidelines of Research Animal Resource Center of Memorial Sloan Kettering Cancer Center (IACUC: 06-07-012). All patient-derived tissues were collected in compliance with rules and regulations of Memorial Sloan Kettering Cancer Center (IRB: 12001).

1. Medium and buffer preparation

  1. Thaw basement membrane matrix (e.g., Matrigel) at 4 °C overnight before starting the experiment. Keep it on ice during use.
  2. Place culture plates at 37 °C for 24 h prior to experiments. This will help the basement membrane matrix dome (hereafter referred to as matrix dome) to polymerize. Plating organoids is described in step 2.1.2.
  3. Prepare the organoid medium according to the established protocol5.
  4. Prepare the organoid medium without the addition of epidermal growth factor (EGF; see Table of Materials for components). EGF suppresses the AR transcriptional output and confers anti-androgen resistance5.
  5. Prepare Dulbecco's Modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS).
    NOTE: This media is used to inhibit the enzymatic digestion with trypsin replacement in sections 2-4.
  6. Prepare drug solutions according to the manufacturer's protocol. For enzalutamide/mdv3100 (hereafter referred to as second generation anti-androgen), prepare a stock solution of 100 µM in dimethyl sulfoxide (DMSO). Stock can be stored at -20 °C for up to 6 months and does not have to be made fresh.

2. Isolation, enzymatic digestion, and establishment of organoids

  1. Isolate prostate organoids from mouse or human tissue according to the previously established protocols5,7. A brief description is provided below.
    1. Mince and enzymatically digest prostate tissue to produce a single cell suspension. In this experiment, 1 mL of 5 mg/mL collagenase type II in ADMEM/F12 was used for the digestion of 50 mg of prostate tissue.
    2. Collect cells by centrifugation at 300 x g for 5 min, count the cells, resuspend them in the basement membrane matrix, and plate at the appropriate density5,7 in the matrix domes on pre-warmed organoid culture plates (plating method is shown in Figure 1A).
    3. Allow the domes to solidify and add media onto the tops of the domes so that they are completely covered.
  2. Grow organoids to the desired quantity for downstream applications. Cell number can be determined by standard counting methods. See the application-specific section of the protocol for additional details on density.
  3. Using a P1000 pipette, draw up the medium and pipette up and down to disrupt. When basement membrane matrix is fully disrupted, transfer the suspension to a 15 mL conical tube. Do not place more than 10 domes per single 15 mL conical tube. Centrifuge at 300 x g for 5 min.
  4. Draw off the supernatant and wash the cell pellet with 5 mL of PBS. Centrifuge at 300 x g for 5 min.
  5. Draw off the supernatant and resuspend the pellet in 4 mL of trypsin replacement. Digest for 5-10 min with shaking at 37 °C. Add an equal volume of organoid medium + 10% FBS to inhibit the trypsin replacement. Centrifuge at 300 x g for 5 min.
  6. Draw off the supernatant and resuspend in 1 mL of PBS.
  7. Filter the suspension with a 40 µm filter to ensure a single cell suspension. Quantify the cell number using a hemocytometer or equivalent counting device.
    NOTE: If obtaining viable single cells is difficult, use flow sorting to obtain a single cell solution.

3. Assessing organoid formation capacity

NOTE: To determine the percentage of cells that can generate an organoid, a seeding assay can be performed as a proxy for the stem/progenitor potential. The organoid formation capacity is also important for defining a cell seeding number for the viability assays.

  1. Dilute the cell suspension obtained in step 2.7 to 100 cells per 10 µL of the suspension using organoid medium containing 10 µM Rho kinase inhibitor Y-27632.
  2. Transfer 1,100 cells (110 µL of suspension) to a new conical tube.
  3. Add 285 µL of basement membrane matrix and resuspend the cells. This will result in a ~70% matrix concentration.
    NOTE: Dilution of the basement membrane matrix during seeding greatly reduces the variation in dome size, caused by the viscosity of the protein matrix.
  4. Seed cells in 35 µL of matrix domes in a pre-warmed 24 well plate, resulting in 200 cells/well. Plate 3-5 replicates per sample (also see plating method in Figure 1A and step 2.1.2).
  5. To ensure that the cells remain within the matrix dome, flip the plate and place it in a cell incubator to solidify the basement membrane matrix.
  6. After 10 min, remove the plate from the incubator and add medium containing the Rho kinase inhibitor.
  7. Refresh the medium every 2 days. After 7 days, quantify the number of organoids. Keep the Rho kinase inhibitor in media throughout the experiment.
  8. Count the number of organoids established per dome and calculate the percent of organoids formed out of the total number of cells plated (200 cells).
    NOTE: Organoid establishment ratios vary from 3%-60% depending on the cell type and genotype.

4. Determining pharmacological responses of organoids

  1. Continuing from step 2.7, seed 1,000-10,000 cells in a matrix dome. Use the organoid formation efficiency and growth speed as a proxy for determining the final cell number.
    NOTE: Recommended cell numbers are provided in Table 1. Use three to five replicates per condition per analysis. Use a final concentration of 70% basement membrane matrix to reduce pipetting errors induced by the viscosity.
  2. Seed 35 µL of matrix domes in a 24 well plate and let the domes solidify as done in section 3 (also see plating method in Figure 1A and step 2.1.2). Add medium containing the Rho kinase inhibitor and drug of choice. This method can be applied to all drugs, but in this protocol, a second-generation anti-androgen is used at 10 µM for an example. To determine half maximal inhibitory concentration (IC50), perform a log10 incremental, and as a control, use the vehicle in which the drug was dissolved.
  3. Refresh the medium every two or three days and analyze the organoids on day 7 to determine the pharmacological response of the drug. The timepoints may vary among the choice of experiment and drug.
    NOTE: Organoids do not have to be trypsinized to perform these assays.
  4. To keep organoids intact, using a P1000 pipette, draw up the medium and pipette up and down to disrupt the basement membrane matrix.
  5. When the basement membrane matrix is fully disrupted, transfer the suspension to a 15 mL conical tube. Do not transfer more than 10 matrix domes per 15 mL conical tube.
  6. Centrifuge at 300 x g for 5 min. Draw off the supernatant and wash with 5 mL of PBS.
  7. Resuspend organoids in 1 mL of PBS and disrupt the organoids using trituration and a glass Pasteur pipette.
  8. Quantify the number of organoid fragments. Seed 5 replicates containing 100 organoid fragments as described in step 2.1.2.
  9. Perform the cell viability assay as described below in section 7.

5. RNA isolation from organoids

NOTE: Commercially available column-based methods yield good quantity and quality of RNA. To ensure good quantity RNA, use a minimum of one dome per sample; however, using three domes is recommended, which can be seeded in a single well of a 12 well plate.

  1. Add ß-mercaptoethanol (1%) to the glutathione lysis buffer in the RNA isolation kit.
  2. Draw off the medium from the basement membrane domes containing organoids and add 750 µL of this buffer. Pipette up and down using a P1000 pipette. Check that all the basement membrane matrix has been dissolved.
  3. Add 750 µL of 70% ethanol and mix by pipetting. Subsequently transfer 700 µL of the mixture to the column, centrifuge at 12,000 x g for 1 min, and repeat with the remainder of the lysate.
  4. Perform washes and on-column DNase treatment according to manufacturer's instructions. Elute RNA in 30-50 µL of RNAse-free water.
  5. Measure the concentrations using a fluorometer at OD = 260 nm and 280 nm and store at -80 °C or continue with downstream applications.

6. Protein isolation from organoids

NOTE: For protein isolation, prepare standard RIPA buffer containing phosphatase and protease inhibitors (Table of Materials). Using at least three domes is recommended, which can be seeded in a single 12 well.

  1. Using a P1000 pipette, draw up the medium from the cell with the basement membrane domes containing organoids and pipette up and down to disrupt the basement membrane matrix.
  2. When fully disrupted, transfer the suspension to a 15 mL conical tube. Centrifuge at 300 x g for 5 min.
  3. Draw off the supernatant and wash with 5 mL of ice-cold PBS. Centrifuge at 300 x g for 5 min.
  4. Draw off the supernatant and resuspend the pellet in 4 mL of trypsin replacement. Digest for 5-10 min while shaking at 37 °C.
  5. Add an equal volume of organoid medium + 10% FCS to inhibit the trypsin replacement. Centrifuge at 300 x g for 5 min.
    NOTE: Post-centrifugation, no basement membrane matrix should be visible in the pellet.
  6. Draw off the supernatant and wash with 5 mL of ice-cold PBS. Draw off the supernatant and resuspend the cell pellet in 300 µL of lysis buffer using a P1000 pipet, then transfer to a 1.5 mL microcentrifuge tube.
  7. Incubate on ice for 10 min and subsequently sonicate 2x for 30 s each at cooled water with a temperature of 4 °C. Place the tube back on ice and perform protein quantification using standard methods.
  8. Denature the protein by adding sodium dodecyl sulfate (SDS) containing loading dye and boil for 5 min at 95 °C. Store lysates at -80 °C or continue with downstream applications.

7. Cell viability assay with organoids

NOTE: Cell viability can be assessed using the commercially available cell viability assay kit and a luminometer. Prepare buffers according to the manufacturer's instructions. Five replicates per condition is recommended: one replicate consisting of one 35 µL basement membrane matrix dome in one well of a 24 well plate.

  1. Draw off the medium of the organoid culture, being careful to leave the matrix domes intact.
  2. Add 65 µL of PBS and pipette up and down to disrupt the matrix dome.
  3. Add 100 µL of the cell viability assay kit buffer and resuspend by pipetting.
  4. Incubate at room temperature (RT) for 10 min with shaking.
  5. Transfer 100 µL of mixture to a non-translucent plate suitable for the luminometer and perform reading according to the manufacturer's instructions for the cell viability assay kit.

8. Preparation of organoids for xenografting

NOTE: Organoids are also amenable for subcutaneous grafting in both immune compromised animals, as well as, isogenic mice. To ensure injected organoids are distinguishable in vivo, label organoids with a constitutively expressing fluorophore5. It is recommended to perform a pilot experiment for grafting using 5 x 105 cells to 2 x 106 cells per injection, with increments of 5 x 106 cells, as grafting efficiency varies between organoid lines.

  1. Using a P1000 pipette, draw up the medium and pipette up and down to disrupt the basement membrane matrix. When fully disrupted, transfer the suspension to a 15 mL conical tube. Centrifuge at 300 x g for 5 min.
    NOTE: Do not transfer more than 10 matrix domes per 15 mL conical tube.
  2. Draw off the supernatant and wash with 5 mL of PBS. Centrifuge at 300 x g for 5 min.
  3. Draw off the supernatant and resuspend the pellet in 4 mL of trypsin replacement. Digest for 5-10 min while shaking at 37 °C.
  4. Add equal volume of organoid medium + 10% FBS to inhibit trypsin replacement. Centrifuge at 300 x g for 5 min.
  5. Draw off the supernatant and resuspend in 1 mL of PBS. Filter the suspension with a 40 µm filter to ensure a single cell suspension. Quantify cells using standard methods.
  6. Spin down and resuspend the cells in PBS + Rho inhibitor to a concentration of 2 x 106 cells per 100 µL (see Table 2 for cell concentrations and absolute cell number needed for varying concentrations). Use an equal volume of basement membrane matrix to generate a 1:1 suspension. Place the suspension on ice.
  7. Inject cells according to standard protocols and monitor xenograft growth using standard methods8.

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Results

Seeding efficiency
Organoid formation capacity is determined by phenotype and genotype. Wild-type (WT) prostate basal cells showed superior organoid formation capacity (30%-40%) compared to luminal cells (3%) (Figure 1A). After organoid establishment, the formation capacity increased drastically. Typically, 25%-30% of cells derived from a WT organoid can form a new organoid (Figure 1B...

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Discussion

Understanding the molecular mechanisms underlying anti-androgen resistance and discovering potential therapeutic vulnerabilities requires testing of pharmacological responses in model systems mimicking prostate cancer. Described here is a detailed protocol for the reliable analysis of pharmacological responses in patient-derived and genetically engineered prostate organoids and preparation of these organoid samples for downstream applications.

There are two critical steps in this protocol. The...

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Disclosures

C.L.S serves on the board of directors of Novartis; is a cofounder of ORIC Pharmaceuticals and coinventor of enzalutamide and apalutamide; is a science advisor to Agios, Beigene, Blueprint, Column Group, Foghorn, Housey Pharma, Nextech, KSQ, Petra, and PMV; and is a cofounder of Seragon, purchased by Genentech/Roche in 2014. W.R.K. is a coinventor and patent holder of organoid technology.

Acknowledgements

K.P. is supported by NIH 1F32CA236126-01. C.L.S. is supported by HHMI; CA193837; CA092629; CA224079; CA155169; CA008748; and Starr Cancer Consortium. W.R.K. is supported by Dutch Cancer Foundation/KWF Buit 2015-7545 and Prostate Cancer Foundation PCF 17YOUN10.

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Materials

List of materials used in this article
NameCompanyCatalog NumberComments
A83-01Tocris2939Organoid medium component: Final concentration 200 nM
ADMEM/F12Gibco/Life technologies12634028Organoid medium component
B27Gibco/Life technologies17504-044Organoid medium component
Cell culture platesFisher657185
Cell Titer GloPromegaG7571
DHTSigma-AldrichD-073Organoid medium component: Final Concentration 1 nM
DMSOFisherBP231-100
EGFPeprotech315-09Organoid medium component: Final concentration 50 ng/ml for mouse, 5 ng/nl for Human
FGF10Peprotech100-26Human specific organoid medium component: Final concentration 10 ng/ml
FGF2Peprotech100-18BHuman specific organoid medium component: Final concentration 5 ng/ml
GlutamaxGibco/Life technologies35050079Organoid medium component
HEPESMADE IN-HOUSEN/AOrganoid medium component: Final concentration 10 mM
Matrigel (Growthfactor reduced & Phenol Red free)CorningCB-40230COrganoid medium component
N-AcetylcysteineSigma-AldrichA9165Organoid medium component: Final concentration 1.25 mM
NicotinamideSigma-AldrichN0636Human specific organoid medium component: Final concentration 10 mM
NOGGINPeprotech or stable transfected 293t cells with Noggin construct (Karthaus et al. 2014)120-10COrganoid medium component: Final Concentration 10% conditioned medium or 100 ng/ml
Penicillin/StreptavidinGemini Bio-Products400-109Organoid medium component
Phospatase inhibitorsMerck Millipore524629
Prostaglandin E2Tocris3632464
Protease InhibitorsMerck Millipore539131
R-SPONDINPeprotech or stable transfected 293t cells with R-Spondin1 construct (Karthaus et al. 2014)120-38Organoid medium component: Final Concentration 10% conditioned medium or 500 ng/ml
RIPA bufferMerck20-188
RNA-easy minikitQiagen74104
SB202190Sigma-Aldrich152121-30-7Human specific organoid medium component: Final concentration 10 μM
TryplEThermoFisher12605036
Y-27632SelleckchemS1049Organoid medium component: Final Concentration 10 μM

References

  1. Robinson, D., et al. Integrative Clinical Genomics of Advanced Prostate Cancer. Cell. 162 (2), 454(2015).
  2. Arora, V. K., et al. Glucocorticoid Receptor Confers Resistance to Antiandrogens by Bypassing Androgen Receptor Blockade. Cell. 155 (6), 1309-1322 (2013).
  3. Ku, S. Y., et al. Rb1 and Trp53 cooperate to suppress prostate cancer lineage plasticity, metastasis, and antiandrogen resistance. Science. 355 (6320), 78-83 (2017).
  4. Mu, P., et al. SOX2 promotes lineage plasticity and antiandrogen resistance in TP53- and RB1-deficient prostate cancer. Science. 355 (6320), 84-88 (2017).
  5. Karthaus, W. R., et al. Identification of Multipotent Luminal Progenitor Cells in Human Prostate Organoid Cultures. Cell. 159 (1), 163-175 (2014).
  6. Gao, D., et al. Organoid Cultures Derived from Patients with Advanced Prostate Cancer. Cell. 159 (1), 176-187 (2014).
  7. Drost, J., et al. Organoid culture systems for prostate epithelial and cancer tissue. Nature Protocols. 11 (2), 347-358 (2016).
  8. Bose, R., et al. ERF mutations reveal a balance of ETS factors controlling prostate oncogenesis. Nature. 546 (7660), 671-675 (2017).
  9. Platt, R. J., et al. CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling. Cell. 159 (2), 440-455 (2014).
  10. Carver, B. S., et al. Reciprocal feedback regulation of PI3K and androgen receptor signaling in PTEN-deficient prostate cancer. Cancer Cell. 19 (5), 575-586 (2011).
  11. Puca, L., et al. Patient derived organoids to model rare prostate cancer phenotypes. Nature Communications. 9 (1), 2404(2018).
  12. Gao, D., et al. Organoid Cultures Derived from Patients with Advanced Prostate Cancer. Cell. 159 (1), 176-187 (2014).
  13. Puca, L., et al. Delta-like protein 3 expression and therapeutic targeting in neuroendocrine prostate cancer. Science Translational Medicine. 11 (484), eaav0891(2019).
  14. Dijkstra, K. K., et al. Generation of Tumor-Reactive T Cells by Co-culture of Peripheral Blood Lymphocytes and Tumor Organoids. Cell. 174 (6), 1586-1598 (2018).
  15. van de Wetering, M., et al. Prospective derivation of a living organoid biobank of colorectal cancer patients. Cell. 161 (4), 933-945 (2015).
  16. Sato, T., et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature. 459 (7244), 262-265 (2009).
  17. Barker, N., et al. Lgr5(+ve) stem cells drive self-renewal in the stomach and build long-lived gastric units in vitro. Cell stem cell. 6 (1), 25-36 (2010).
  18. Bartfeld, S., et al. In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection. Gastroenterology. 148 (1), 126-136 (2015).
  19. Huch, M., et al. Long-term culture of genome-stable bipotent stem cells from adult human liver. Cell. 160 (1-2), 299-312 (2015).
  20. Boj, S. F., et al. Organoid models of human and mouse ductal pancreatic cancer. Cell. 160 (1-2), 324-338 (2015).
  21. Schutgens, F., et al. Tubuloids derived from human adult kidney and urine for personalized disease modeling. Nature Biotechnology. 37 (3), 303-313 (2019).
  22. Sachs, N., et al. A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity. Cell. , 1-25 (2017).

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Organoid CulturePharmacological ResponseGenotype AnalysisDrug TreatmentViability AssayProtein IsolationRNA IsolationXenografting AssayCRISPR Cas9
Prostate Organoid Cultures as Tools to Translate Genotypes and Mutational Profiles to Pharmacological Responses
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