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20 protocols using rmil 7

1

Ryk-mediated T-cell development in vitro

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In total, 50 000 total FL cells were obtained from Ryk WT and Ryk KO mice and were co-cultured on confluent layers of OP9 WT/DL1, OP9 Wnt3a/DL1, or OP9 Wnt5a/DL1 mixed in a 1:1 ratio as described previously27 (link) with Alpha MEM 10% FCS containing 50 ng/ml rmSCF, 10 ng/ml rmFlt3L and 10 ng/ml rmIL-7 (all cytokines from R&D Systems, Abinsdon, UK) in 24-well plates. Cells were harvested after 7 and 14 days of co-culture and assessed for T-cell development by flow cytometric analysis. FTOC were done as described before47 (link) using fetal thymic lobes from E14 embryos, which were genotyped for the status of the Ryk deficiency. Thymic lobes were cultured on a nitrocellulose filter on air/medium interphase for 7–14 days, dispersed, and analyzed by flow cytometry.
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2

Culturing Murine ILC1s with Crypts

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Approximately 1500-2500 murine ILC1 were seeded with ~100 mechanically disrupted SIO crypts per well, resuspended in 30μl ice-cold Matrigel, pipetted onto pre-heated tissue culture plates (Nunclon) and incubated at 37°C for 15-20min prior to addition of pre-warmed basal media supplemented with 50mM B2ME (R&D), 20ng/ml rhIL-2 (Sigma), 20ng/ml rmIL-7 (R&D), and 1ng/ml IL-15 (R&D), with media changes every 2-4 days.
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3

OP9 Co-Culture Conditions for Hematopoietic Differentiation

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For different experiments various conditions of OP9 co-cultures were used as follows: OP9-WT, OP9-DL1-GFP, OP9-WT/DL1 (1 : 1), OP9-DLW3A, OP9-DLW5A, OP9-DLW3A/DL1 (1:1), OP9-DLW3A/DL1 (1 : 10) and OP9-DLW3A/DL1 (1 : 100). In all conditions 50 000 total fetal liver cells were cultured on confluent layers of OP9 cells, with AlphaMEM 10% FCS containing 50 ng/ml rmSCF, 10 ng/ml rmFlt3L and 10 ng/ml rmIL-7 (all cytokines from R&D systems, Minneapolis, MN, USA) in a well of 24-wells plate. For different purposes, cells were harvested after 6 h, 24 h, 3, 7 or 14 days of culture and stained for flow cytometric analysis.
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4

Evaluating NK cell activation and function

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Splenic lymphocytes were prepared and cultured with cytokines (rmIL-15 100ng/ml; rmIL-12 25ng/ml; rmIL-18 5ng/ml; hTGFb1 5ng/ml; rmIL-7 20ng/ml from R&D Systems or rmIFNb 100U/ml from PBL), or on antibody coated plates (anti-NKp46, anti-NK1.1, anti-Ly49D, anti-NKG2D, anti-Ly49C/I, anti-NKG2A, all at 10μg/ml) and Golgi-stop (BD-Biosciences) in the presence of anti-CD107a for 4h. Surface and intracellular stainings were then performed and IFN-γ production as well as CD107a exposure was measured by flow cytometry.
Human whole blood samples from healthy donors were collected by venous puncture in heparin containing vials. PBMCs were then isolated by Ficoll gradient centrifugation and stimulated for 36h at 37°C using 1.000UI/mL rhIL-2 in the presence or absence of mTOR inhibitors. Intracellular stainings for pS6, GzmB and Perforin were performed using the FoxP3 Fixation/Permeabilization Concentrate and Diluent (eBioscience).
Rapamycin (Sigma-Aldrich; 10 to 100nM), PP242 (Sigma-Aldrich; 1μM) and Ku-0063794 (Stemgent; 3μM) were used.
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5

Culturing Murine ILC1s with Crypts

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Approximately 1500-2500 murine ILC1 were seeded with ~100 mechanically disrupted SIO crypts per well, resuspended in 30μl ice-cold Matrigel, pipetted onto pre-heated tissue culture plates (Nunclon) and incubated at 37°C for 15-20min prior to addition of pre-warmed basal media supplemented with 50mM B2ME (R&D), 20ng/ml rhIL-2 (Sigma), 20ng/ml rmIL-7 (R&D), and 1ng/ml IL-15 (R&D), with media changes every 2-4 days.
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6

Hepatic ILC2 Activation and CD4+ T Cell Interactions

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FACS-isolated hepatic ILC2 (1 × 104) were cultured in the presence of rmIL-33 (10 ng/ml), rmIL-25 (10 ng/ml), rmIL-1β (10–200 ng/ml; all BioLegend), rmIFNγ (10 ng/ml) and rmIL-12 (10–200 ng/ml; both R&D Systems, Wiesbaden, Germany) for 4 days. For ILC2 maintenance, all cultures were done in the presence of rmIL-2 (10 U/ml) and rmIL-7 (10 ng/ml; both R&D Systems). For CD4+ T-cell activation, hepatic ILC2 (2 × 104) were co-cultured with FACS-isolated, OVA-specific CD4+ T cells (1 × 105) or OVA-specific Th1 cells (1 × 105) in the presence of OVA323-339 peptide (5 µg/ml) for 4 days. For blocking IL-2 or IFNγ, co-cultures were done in the presence of an anti-IL-2 (JES-1A12; 10 µg/ml; BD Pharmingen) and anti-IFNγ (R4-6A2; 10 µg/ml; BioXCell, West Lebanon, NH) antibody, respectively.
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7

Organoid-Immune Cell Co-Culture

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Approximately 15-30 mature HIO were added to eppendorfs containing 50-300 hILC1 directly after FACS isolation from biopsies. The two components were centrifuged at 500G for 3min, supernatant was carefully removed, and the co-cultures were resuspended in 35µl Matrigel and plated onto pre-warmed tissue culture treated plates. The same culture conditions optimized for murine co-cultures were used for HIO-hILC1 co-cultures, including 50mM B2ME (R&D), 20ng/ml rhIL-2 (Sigma), 20ng/ml rmIL-7 (R&D), and 1ng/ml IL-15 (R&D), with media changes every 3-4 days.
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8

Lung ILC2 Cell Culture with Cytokines

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5×103 sorted lung ILC2s per well from mice treated with rmIL-7 + anti-human IL-7 were cultured at 37°C and 5% CO2 in Dulbecco’s modified Eagle’s medium (Corning) with 10% fetal bovine serum (Corning), 1% L-glutamine (Corning), 1% penicillin/streptomycin (Corning), 25 mM HEPES buffer (Corning), and 55 μM β-mercaptoethanol (Sigma-Aldrich) with 10 ng/mL rmIL-2 (Thermo Fisher), 10 ng/mL rmIL-7 (R&D Systems) and either 30 ng/mL rmIL-33 (R&D Systems), 100 nmol/mL PGD2 (Cayman Chemical, Ann Arbor, MI), rmlIL-33 + PGD2, or rmIL-33 + PGD2 + the CRTH2-specific inhibitor OC000459 (1 μM)44 (link). PGD2 and OC000459 were dissolved in 100 μL DMSO diluted 1:1000 in PBS. Equal volumes of DMSO were added to all the other treatments as a control. On day 3 and 5 of culture, fresh cytokines were spiked into cultures. On day 6, cells were analyzed by flow cytometry.
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9

Evaluating NK cell activation and function

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Splenic lymphocytes were prepared and cultured with cytokines (rmIL-15 100ng/ml; rmIL-12 25ng/ml; rmIL-18 5ng/ml; hTGFb1 5ng/ml; rmIL-7 20ng/ml from R&D Systems or rmIFNb 100U/ml from PBL), or on antibody coated plates (anti-NKp46, anti-NK1.1, anti-Ly49D, anti-NKG2D, anti-Ly49C/I, anti-NKG2A, all at 10μg/ml) and Golgi-stop (BD-Biosciences) in the presence of anti-CD107a for 4h. Surface and intracellular stainings were then performed and IFN-γ production as well as CD107a exposure was measured by flow cytometry.
Human whole blood samples from healthy donors were collected by venous puncture in heparin containing vials. PBMCs were then isolated by Ficoll gradient centrifugation and stimulated for 36h at 37°C using 1.000UI/mL rhIL-2 in the presence or absence of mTOR inhibitors. Intracellular stainings for pS6, GzmB and Perforin were performed using the FoxP3 Fixation/Permeabilization Concentrate and Diluent (eBioscience).
Rapamycin (Sigma-Aldrich; 10 to 100nM), PP242 (Sigma-Aldrich; 1μM) and Ku-0063794 (Stemgent; 3μM) were used.
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10

Short-term Culture of Sorted γδ Thymocytes

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For short-term culture of sorted γδ thymocytes, OP9-DL1 feeder cells were used. OP9-DL1 cells (gift from J.C. Zúñiga-Pflücker55 (link)) were maintained at 30–80% confluency in OP9 medium (HEPES-buffered Glutamax MEM-α (Life Technologies) containing 20% FBS, penicillin/streptomycin, Na-pyruvate, gentamycin and β-mercaptoethanol) in 10 cc culture dishes (Nunc, Roskilde, Denmark). On the day before the experiments, OP9-DL1 cultures were set up by adding 3 × 103 OP9-DL1 cells per well of a flat-bottom 96-well plate (Nunc, Roskilde, Denmark) and allowed to form monolayers overnight. For anti-CD3-treated cultures, the wells were coated with anti-CD3 prior to seeding OP9-DL1 cells by adding 5 µg per mL anti-CD3 antibody (145-2C11 clone; BioLegend) in PBS to each well and incubated for at least 4 h at 37 °C. The medium was removed, and 2–10 × 103 sorted γδ thymocytes were suspended in 200 µL OP9 medium containing 5 ng per mL rmIL-7, and 5 ng per mL rhFlt-3L (R&D Systems Inc., Minneapolis, USA) and added to each well. OP9-DL1 co-cultures are known to induce artificial phenomena such as fate switching27 (link), 31 (link), 56 (link). To avoid these phenomena and limit the risk of selective outgrowth of minor populations, the cells were only cultured for 2 days before analysis by flow cytometry.
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