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Comprehensive Immune Profiling of T Cells

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Antibodies against human CD3 (BW264/56) and CD45RA (T6D11) were purchased from Miltenyi Biotec. Antibodies against human CD3 (UCHT1), CD25 (BC96), CD127 (A019D5), PD-1 (EH12.2H7), CCR7 (G043H7), and CD155 (SKII.4) were obtained from Biolegend. Fixable viability dye and antibodies against human CD4 (RPA-T4), CD8α (RPA-T8), and Foxp3 (PCH101) were purchased from Thermo Fisher Scientific, and antibody against human CD96v2 (628211) was obtained from R&D Systems. Fluorescently labeled F(ab′)2 against FcγRI (10.1), FcγRIIA/B (AT10), and FcγRIIIA (3G8) were provided by Mark Cragg, University of Southampton. FcγR staining was performed in PBS/1% BSA, without a prior FcγR blocking step. For CFSE proliferation assays and analysis of CD96 and CD155 expression, cells were incubated for 10 minutes at 4°C with 10% heat-inactivated AB serum (MilliporeSigma) prior to surface staining. For TIL phenotyping, cells were incubated with human FcR blocking reagent (Miltenyi Biotec) for 10 minutes at 4°C prior to surface staining. When required, intracellular staining was performed using the Foxp3 staining buffer kit (Thermo Fisher Scientific). Samples were analyzed with a FACSCanto II flow cytometer and DIVA Software (BD Biosciences), FCS Express (De Novo Software), or FlowJo software (version 10).
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Multiparametric Analysis of Cultured Cells

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Cultured cells were harvested and incubated with PerCP Cy5.5-conjugated CD90 (mouse clone Thy1, BioLegend), FITC-conjugated Vimentin (mouse clone RV202, ab8978, Abcam), PE-conjugated PVR (mouse clone SKII.4, BioLegend) or appropriate isotype control at 4°C for 30 min, washed twice, and analyzed using a BD FACS Calibur cytometer. The results were analyzed using Kaluza software.
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Quantitative Flow Cytometry Analysis

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Flow cytometry analysis was performed on an LSRFortessa (BD, USA). Cells were grown in the medium indicated previously, harvested by using Stem Cell Pro Accutase (Invitrogen). Phycoerythrin (PE)-conjugated monoclonal antibodies WM15, IM7 (both Invitrogen), CC2C6, MIH42, MIH2, JS11, SKII.4, P1E6-C5, GoH3, and SHM16 (all Biolegend) directed against CD13, CD44, CD47, CD276/B7-H3, CD274/PD-L1, CD55, CD155, CD49b, CD49f, and EPHA2 were used for detection of osteosarcoma surface markers. PE-conjugated MOPC-21 (Biolegend) were used as isogenic control. A minimum of 30,000 events were recorded. Quantification was performed using BD Quantibrite PE-conjugated beads (BD Biosciences) according to the manufacturer’s protocol. Quantitative data is provided (Supplemental Figure 4).
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Multiparametric Flow Cytometry for CAR T-cell Analysis

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Before staining with relevant fluorochrome-conjugated Abs, cells were treated with Human TruStain FcX (Fc receptor blocking solution; BioLegend, San Diego, CA, USA, #422302). Abs against CD4 (APC; OKT4; #317416), CD8 (PerCP-Cy5.5; HIT8a; #300924), TIGIT (PE-Cy7; A15153G; #372713), CD226 (FITC; 11A8; #338303), CD155 (Alexa Fluor 647; SKII.4; #337621), CD111 (PE; R1.302; #340404), HER2 (PE; 24D2; #324405) and mouse IgG1 κ isotype control (PE; MOPC-21; #400113) were from BioLegend, San Diego, CA, USA. Ab against CD96 (PE; NK92.39) was from eBioscience, Thermo Fisher Scientific, Waltham, MA, USA (#12-0969-42) or BioLegend, San Diego, CA, USA (#338405). Cell surface expression of CAR was detected by incubation with recombinant biotinylated protein L (ACROBiosystems, Newark, DE, USA, #RPL-P814R) followed by incubation with PE-conjugated streptavidin (eBioscience, Thermo Fisher Scientific, Waltham, MA, USA, #12-4317-87). To exclude dead cells, 4′,6-diamidino-2-phenylindole dihydrochloride (DAPI; Biolegend, San Diego, CA, USA, #422801) was used. Samples (at least 20,000 events) were acquired on a LSRII cytometer (BD Biosciences) or MACSQuant X (Miltenyi Biotec) and analyzed with FlowJo software (TreeStar, BD Life Sciences, Franklin Lakes, NJ, USA).
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