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27 protocols using gastrin 1

1

Establishment of Pancreatic Cancer Organoids

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Between 2014 and 2017, tumor samples were collected from human pancreatic ductal adenocarcinoma cancer (PDAC) patients under IRB12-1108 and IRB13-1149. Samples were obtained from patients undergoing pancreatic resections at The University of Chicago Medicine (UCM) facilities. Tumor samples were digested and established into organoids according to established protocols previously published9 (link). Briefly, organoids were grown and cultured by embedding dissociated tumor cells in growth-factor-reduced (GFR) Matrigel (Corning, 356231) and cultured in complete media (Intesticult [Stemcell Technologies, 6005], A83-01 [0.5 µM, Sigma, SML0788], fibroblast growth-factor 10 [FGF10, 100 ng/ml, Gibco, PHG024], Gastrin I [10 nM, Sigma, 17105-041], N-acetyl-L-cysteine [10 mM, Sigma, A9165], Nicotinamide [10 mM, Sigma, N0636], B27 supplement [1x, Gibco, 17504-044], Primocin [1 mg/ml, InvivoGen, ant-pm-1], and Y-27632 [10.5 μM Tocris, 1254]). Organoids were passaged via mechanical dissociation and TrypLE Express (Fisher Scientific, 12605-010) to single cells before being loaded on to the platform.
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2

Generation of Stable Colorectal Organoids

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Briefly, UCB tumor tissues were minced at about 0.5 cm diameter and disassociated into individual cells via digestion with 5 mg/mL collagenase type II (Life Technologies) with 10 μM Y-27632 dihydrochloride and incubated at 37 °C for 1 h. Then, we filtered the suspension of dissociated cells through a 70 μm mesh filter. The UCB cells were then embedded in Matrigel and cultured with Advanced Dulbecco's modified Eagle's medium/F12 mixed with 500 ng/mL Rspo1, 100 ng/mL Noggin, 50 ng/mL EGF, 10 mM nicotinamide, 500 nM A830-1 (Tocris), 3 mM SB202190 (Sigma), 10 nM prostaglandin E2 (Sigma), penicillin/streptomycin, 10 mM HEPES, 2 mM GlutaMAX, 1 × B27 (Life Technologies), 10 nM gastrin I (Sigma), and 1 mM N-acetylcysteine (Sigma) at 37 °C under 5% CO2. The medium was obtained from OuMel (Hai Shang, China). For the generation of stable lines, organoids were first digested into individual cells by TrypLE (GIBICO) and incubated with purified lentivirus for 6 h, followed by selection with 2 μg/mL puromycin. For organoids formation assay, the individual organoid cells were seeded onto a 24-well plate with a density of 1000 cells in 50 μL/well. The number and size of the organoids were determined after 2 weeks, and the growth area of organoids was measured and quantified by ImageJ.
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3

Culturing Human Intestinal Organoids

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Polyps were dissociated and washed as described in the COLON MAP scRNA-seq, Encapsulation and Library Generation section. After dissociation, cells were washed 3 times with PBS containing 10 μM ROCK inhibitor (STEMCELL Technologies) and pelleted by quick-pulse centrifugation for 7 s. Human organoid models were generated from COLON MAP individuals of both sexes (70% female, 30% male). Polyp-derived cells were grown with Human IntestiCult organoid growth media (STEMCELL Technologies) supplemented with 10 μM Y-27632, 10 nM Gastrin I (Sigma-Aldrich), 1 mM N-acetyl-L-cysteine (Sigma-Aldrich), 500 nM A83–01 (Tocris), 50 ng/mL FGF-2 (Thermo Fisher), 100 ng/mL IGF-1 (BioLegend), 100 μg/mL Primocin (InvivoGen), and Matrigel (Corning) in a 3:1 ratio of Matrigel to media. Media was replaced every 2–3 days, and passaging was performed by dissociating the organoids in TrypLE Express (Thermo Fisher) with 10 μM Y-27632 for 15 minutes at 37°C while shaking and triturating.
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4

Culturing Human Colonic Organoids

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This study was approved by the Institut Pasteur’s ethical and medical committee under the agreement N°2012-37. Surgically resected human colonic tissues were obtained from the Henri Mondor Hospital. All samples were obtained from patients who provided informed consent before surgery. Normal epithelia were isolated and cultured according to the protocol described by Sato et al., with minor modifications36 (link). Organoids were cultured with Advanced DMEM/F12 (ThermoFisher) supplemented with Hepes (ThermoFisher), 2 mM GlutaMAX (ThermoFisher), 100 U/mL penicillin and 100 μg/mL streptomycin (ThermoFisher), 1× N2 and B27 supplements (ThermoFisher), 1 mM N-acetyl-L-cysteine (Sigma), 10 μM Y-27632 (Sigma), 500 nM A83-01 (Tocris), 10 μM SB202190 (Sigma), 10 mM nicotinamide (Sigma), 10 nM gastrin I (Sigma), 100 ng/mL recombinant human Noggin (R&D Systems), 50 ng/mL recombinant human EGF (R&D Systems), 1 μg/mL recombinant human R-Spondin-1 (Peprotech), 100 ng/mL recombinant human Wnt-3A (R&D Systems), 3 μM CHIR99021 (Sigma), and 10% (vol/vol) FBS (ThermoFisher), at 37 °C in 5% CO2. Oraganoids were cultured in 48-well plates, 100 crypts per well. RNA was isolated using the RNeasy Mini kit and the RNase free DNase kit (Qiagen). Gene expression was analyzed using primers purchased from Sigma. Data were normalized to the B2M housekeeping gene expression.
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5

Organoid Culture and Viability Assay

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Organoids were dissociated into single cells with TrypLE Express Enzyme (ThermoFisher). Cells were counted and diluted to 10 cells/μl in a mixture of experimental medium: AdDMEM/F12 medium supplemented with HEPES (1x, Invitrogen), Glutamax (1x, Invitrogen), penicillin/streptomycin (1x, Invitrogen), B27 (1x, Invitrogen), R-spondin-conditioned medium (10% v/v, Calvin Kuo), mNoggin (0.1 μg/ml, Peprotech), Gastrin I (10 nM, Sigma), fibroblast growth factor 10 (FGF10, 0.1 μg/ml, Preprotech), Nicotinamide (10 mM, Sigma), and A83–01 (0.5 μM, Tocris) and Growth factor-reduced Matrigel (BD, 10% final concentration). 150 μLof this mixture (1500 cells per well) was plated in 96-well white plates (Nunc), whose wells had been previously coated with poly(2-hydroxyethyl methacrylate) (Sigma) to prevent cell adhesion to the bottom of the wells. Cell viability was measured every 24 h using the Cell-Titer-Glo assay (Promega) and SpectraMax I3 microplate reader (Molecular Devices). Five replicate wells per time point were measured.
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6

Establishment of Patient-Derived Colorectal Cancer Organoids

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Fresh CRC tumour tissue was obtained with informed patient consent, as approved by the Research Ethics Board at the University Health Network in Toronto. Fresh tumour tissue was cut into small pieces and digested with Liberase (TH grade; Roche) for 90 min at 37 °C, and dissociated cells were collected and embedded in growth factor-reduced Matrigel (Corning). The Matrigel and embedded cells were overlaid with growth medium containing advanced DMEM/F-12 (Gibco) supplemented with 2 mM GlutaMAX (Gibco), 10 mM HEPES (Gibco), 100 U/ml penicillin–streptomycin (Gibco), 1 × B-27 Supplement (Gibco), 1.25 mM N-acetyl-L-cysteine (Sigma), 10 nM Gastrin I (Sigma), 50 ng/ml mouse EGF (Gibco), and 500 nM A83-01 (Tocris). All organoid models were authenticated using short tandem repeat profiling, and proven to be negative for mycoplasma. Organoids were kept in culture for a maximum of 8–10 passages.
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7

Culturing Human Intestinal Organoids

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Polyps were dissociated and washed as described in the COLON MAP scRNA-seq, Encapsulation and Library Generation section. After dissociation, cells were washed 3 times with PBS containing 10 μM ROCK inhibitor (STEMCELL Technologies) and pelleted by quick-pulse centrifugation for 7 s. Human organoid models were generated from COLON MAP individuals of both sexes (70% female, 30% male). Polyp-derived cells were grown with Human IntestiCult organoid growth media (STEMCELL Technologies) supplemented with 10 μM Y-27632, 10 nM Gastrin I (Sigma-Aldrich), 1 mM N-acetyl-L-cysteine (Sigma-Aldrich), 500 nM A83–01 (Tocris), 50 ng/mL FGF-2 (Thermo Fisher), 100 ng/mL IGF-1 (BioLegend), 100 μg/mL Primocin (InvivoGen), and Matrigel (Corning) in a 3:1 ratio of Matrigel to media. Media was replaced every 2–3 days, and passaging was performed by dissociating the organoids in TrypLE Express (Thermo Fisher) with 10 μM Y-27632 for 15 minutes at 37°C while shaking and triturating.
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8

CTC-Derived Organoid Culture Protocol

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To generate the CTC derived organoid, CAF were first seeded on CAF-derived 3D ECMs one day before. Then the fresh isolated CTC were seeded on the cultures. CTC derived Organoid was cultured as previously described without TGF-β modulators 5, it use Advanced DMEM F12 (Gibco) containing 1X antibiotic-antimycotic (Gibco) as base. Supplements include the following: N-acetyl-L-cysteine (NAC; Sigma-Aldrich), human gastrin 1 (Sigma-Aldrich), Gastrin I(Sigma-Aldrich), Nicotinamide (Sigma-Aldrich), R-spondin 1 (Peprotech), EGF(Peprotech) and FGF-10(Peprotech).
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9

Isolation and Culture of Pancreatic Organoids

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Tumor tissues were collected and minced into 2–3 mm3 fragments in basic medium [AdDMEM/F12 (Gibco), 1X Hepes (Gibco, #15630), 1X glutamax (Gibco, #35050061), 100 μg/mL piromocin (InvivoGen, #ant-pm-1)]. Tissue fragments were digested in basic media supplemented with 1 mg/mL liberase (TH; Roche, #5401135001), 10 μg/mL DNase I (Sigma, #4263), and 10 μmol/L ROCK inhibitor (Tocris, #1254) for 30 minutes in 37°C.
Digested tissues were filtered and washed with phosphate-buffered saline containing 5% serum to deactivate the enzymes. Pancreatic cells were mounted in matrigel (Corning, #356231) and were cultured in serum-free organoid growth media composed of basic medium supplemented with 1 mmol/L N-acetyl L-cysteine (Sigma, #A9165), 1 mmol/L nicotinamide (Sigma, #N0630), 100 ng/mL mouse recombinant NOGGIN (PeproTech, #250-38), 500 ng/mL recombinant RSPONDIN (PeproTech, #120–38), 25% serum-free WNT conditioned media (21 ), 50 ng/mL mouse recombinant EGF (Gibco, #PMG8041), 100 ng/mL FGF10 (PeproTech, #100-26), 10 nmol/L gastrin I (Sigma, #G9020), 500 nmol/L A83-01 (Tocris, #2939), and 10 μmol/L Y-27632 dihydrochloride (Tocris, #1254).
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10

Cultivation of Pancreatic Cancer Organoids

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Panc163 cells have been previously established from a primary human PDAC xenograft model and were a generous gift from Bruno Sainz (Rubio-Viqueira et al., 2006 (link)). Cells were maintained as organoids in a Matrigel based culture, medium was changed twice a week, and organoids were split every 10 days using Collagenase/Dispase (Roche) and Accutase (Sigma) as described in more detail in the PDLO culture section. For cultivating PDAC organoids, the medium described by Tiriac et al. (2018) (link) was used: DMEM/F12 medium was supplemented with 1x HEPES, 1x GlutaMAX, 1x P/S, 1x B27, 100 μg/ml Primocin (all Thermo), 1.25 mM N-acetyl-L-cysteine (Sigma), 50% Wnt3a-conditioned medium, 10% RSPO1-conditioned medium, 100 ng/ml recombinant Noggin (PeproTech), 50 ng/ml EGF (R&D), 10 nM Gastrin I (Sigma), 100 ng/ml FGF10 (R&D), 10 mM nicotinamide (Sigma), and 500 nM A83–01 (Tocris). Panc163 were used in qPCR, IF and FC analysis, CFTR and CA assay and RNA-seq experiments as control to PDLOs.
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