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8 protocols using ultra low attachment 96 well u bottom plates

1

Phagocytosis Assay of Human and Mouse Macrophages

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For the phagocytosis assay of human primary macrophage, A2780 cells prelabeled with CFSE (Thermo Fisher, C34554) were cocultured with human macrophages at a ratio of 2:1 for 4 hours in the presence of vehicle control, αCD47-G1 or αCD47-G4 at the dose of 5 μg/ml or supernatants of OV-infected cells at 37 °C in ultra-low-attachment 96-well U-bottom plates (Corning) in serum-free 1640 (Life Technologies). Then the cells were harvested and stained with anti-human CD45 (BD, 552850) to identify macrophages. All flow cytometry data were collected using a Fortessa X20 flow cytometer (BD Biosciences). Phagocytosis was calculated as the number of CD45+CFSE+ macrophages, quantified as a percentage of the total CD45+ macrophages.
For the phagocytosis of mouse macrophages, ID8 or A2780 cells prelabeled with CFSE were cocultured with murine macrophages at a ratio of 2:1 for 6 hours with 5 μg/ml antibodies or supernatants of OV-infected cells at 37°C in ultra-low-attachment 96-well U-bottom plates (Corning) in the serum-free 1640 media (Life Technologies). The cells were harvested. An anti-mouse F4/80 antibody (BD, cat#565787) was used to identify macrophages. Phagocytosis was measured as the number of F4/80+CFSE+ macrophages and quantified as a percentage of the total F4/80+ macrophages.
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2

Tumor Sphere Formation Assay

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For the tumor sphere formation assay, 1 × 103 Caki-1 or 786-O cells were seeded into U-bottom ultra-low attachment 96-well plates (Corning, cat. no. 174925) and cultured in DMEM supplemented with 10% FBS for 2 weeks. Tumor sphere images were captured under a microscope and the area was measured with Image J software (National Institutes of Health).
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3

Fluorescent JEG-3 Trophoblast Spheroids

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Fluorescent spheroids of the trophoblast cell line JEG-3 were generated by transduction with recombinant lentiviral particles expressing GFP from a PGK promoter (Tiscornia et al., 2006) . Briefly, trophoblast cells were grown on 12well plates until cultures reached 70% confluence. Lentiviral particles were added to the culture at a multiplicity of infection (MOI) of 10. Trophoblast cells with the highest GFP levels were collected by fluorescence-activated cell sorting (FACS) and cultured further. To generate spheroids, suspensions of GFP+ JEG-3 cells were adjusted to a 3 × 10 4 cells/ml concentration; 100 µl were seeded in U-bottom ultra-low attachment 96-well plates (Corning, NY, USA) and centrifuged at room temperature for 10 min at 250g. The plates were kept for 48 h at 37°C and 5% CO 2 , resulting in spheroids of around 250 µm diameter.
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4

Cerebral Organoid Generation from Human Embryonic Stem Cells

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Human embryonic stem cells (hESCs) were obtained from WiCell, and cultured in a feeder‐free condition. Cells were maintained with mTeSR medium (Stemcell Technologies) on the Matrigel‐coated 6‐well plates at 37°C supplied with 5% CO2. Cells were cultured and passaged using standard procedures according to the previous description.24 Normal karyotype and contamination‐free were confirmed.
Cerebral organoids were cultured as a previous publication25 with slight modifications. Briefly, H9 hESCs were treated with 0.5 mmol/L EDTA and Accutase to obtain single‐cell suspension. Embryoid bodies (EBs) were generated with 9000 cells/well in the U‐bottom, Ultra low‐attachment 96‐well plates (Corning) with 150 µL of mTeSR medium containing 1xRevitaCell supplement (Gibco) at day 0. Fresh mTeSR medium without RevitaCell supplement was fed to EBs at day 3. At day 5, EBs were transferred into Neural Induction (NI) medium, and medium was exchanged with fresh NI medium every second day for 6 days. EBs were then embedded into Matrigel droplets, and cultured in differentiation medium without vitamin A and shaking. Five days later, cerebral organoids were cultured in differentiation medium supplied with vitamin A on an orbital shaker. Media were exchanged every 5 days until day 30, and used for further experiments.
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5

Macrophage Phagocytic Activity Assay

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Primary human or mouse macrophages were incubated with carboxyfluorescein succinimidyl ester (CFSE)-labeled (Thermo Fisher Scientific, catalog no. C34554) GBM30 or CT2A-hEGFR target cells, respectively, at an effector/target ratio of 1:2 for 6 h in the presence 5 μg ml−1 or 10 μg ml−1 Cmab-h(m)CCL5 fusion protein or IgG1 isotype control in a humidified, 5% CO2 incubator at 37 °C in ultra-low-attachment 96-well U-bottom plates (Corning) in serum-free 1640 media (Life Technologies). The co-cultured cells were harvested by centrifuging them at 400 × g for 5 min at 4 °C and stained with an anti-human CD45 antibody (BioLegend, catalog no. 368516) or an anti-mouse F4/80 antibody (BD Biosciences, catalog no. 565787) to identify human or mouse macrophages, respectively, in flow cytometry assay. Human macrophage phagocytosis was quantified as the percentage of CD45+CFSE+ macrophages among total CD45+ cells. Murine macrophage phagocytosis was quantified as the percentage of F4/80+CFSE+ macrophages among total F4/80+ macrophages. The gating strategy is shown in Supplementary Fig. 2.
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6

In Vitro Phagocytosis Assay for Tumor Cells

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For all flow-based in vitro phagocytosis assays, tumor cells and human macrophages were co-cultured at a ratio of 2:1 in ultra-low-attachment 96-well U-bottom plates (Corning) in serum-free RPMI (Thermo Fisher Scientific). Tumor cells either virally expressed GFP or were labeled with CFSE (Invitrogen) by suspending cells in PBS (5 μM working solution) as per manufacturer instructions for 20 min at 37 °C protected from light and washed twice with 20 ml of FBS-containing media before co-culture. Anti-GD2 (dinutuximab, acquired from United Therapeutics) or anti-B7-H3 (enoblituzumab, acquired from MacroGenics) was added alone or in combination with anti-CD47 (clone B6H12, Bio X Cell) at a concentration of 10 μg ml−1 (or the concentration indicated in the figures). Tumor cells and antibodies were incubated for 30 min in a humidified 5% CO2 incubator at 37 °C. Plates were washed two times; human macrophages were added to the plate; and plates were incubated for 1–2 h at 37 °C. Phagocytosis was stopped by washing with 4 °C PBS and centrifugation at 336g before the cells were stained with Live/Dead stain and anti-CD11b. Assays were analyzed by flow cytometry, and phagocytosis was measured as the number of CD11b+ and CFSE/GFP+ macrophages, quantified as a percentage of the total CD11b+ macrophages and normalized to the control condition.
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7

Tumor Cell Phagocytosis by Macrophages

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All in vitro phagocytosis assays reported here were performed by co-culturing tumor cells and macrophages at a ratio of 200,000 tumor cells to 100,000 macrophages for 2 h in a humidified, 5% CO2 incubator at 37 °C in ultra-low-attachment 96-well U-bottom plates (Corning). Tumor cells expressing fluorescence GFP were collected from plates using TrypLE Express (Life Technologies) before co-culture. After co-culture, phagocytosis assays were stopped. Cells were centrifuged at 400 g for 5 min at 4 °C and stained with APC-labelled anti-CD45 (Clone I3/2.3, BioLegend) to identify macrophages. Assays were analyzed by flow cytometry on Guava easyCyte (Millipore). Phagocytosis was measured as the number of CD45+GFP+ macrophages, quantified as the percentage of the total CD45+macrophages.
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8

Generating Human iPSC-Derived Macrophages

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Human iPSCs derived from umbilical cord blood CD34 + cells (15, (46) (47) (48) were maintained as undifferentiated cells on matrigel-coated tissue culture flasks in mTeSR media (STEMCELL Technologies). Human iPSC-derived macrophages were generated according to previously described protocol (49) with some modifications. Briefly, 8000 human iPSCs were single cell passaged and then aggregated into spin embryoid bodies (EBs) by centrifugation on ultra-low attachment 96-well u-bottom plates (Corning) with cytokines that are essential for hematopoietic progenitor development (APEL media containing 40 ng/mL SCF, 20 ng/mL VEGF, 20 ng/mL BMP4 and 10 μM Rock-Y).
EBs were then manually transferred (20 EBs per well) onto 0.1% gelatin-coated 6-well plates containing differentiation medium I (X-VIVO15 media (Lonza) supplemented with 1% penicillin-streptomycin (Gibco), 1% GlutaMAX (Gibco), 55 mM 2-Mercapnoethanol (Gibco), 50 ng/mL M-CSF and 25 ng/mL IL-3 (all from Peprotech)). Human iPSC-derived macrophage progenitor cells (iPSC-MPro) started to generate after 1-2 weeks. These cells were then collected and further differentiated to mature macrophages (human iPSC-derived macrophages) in differentiation medium II (X-VIVO15 media supplemented with 1% penicillin-streptomycin, 1% GlutaMAX and 100 ng/mL M-CSF) for 7 days.
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