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9 protocols using tnf α fitc

1

Characterizing Anti-CD19 CAR T Cell Responses

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Flow cytometry was performed using a FACSAria II cell counter (BD Biosciences). T cells were assessed for the surface presentation of epitopes with fluorescently labeled monoclonal antibodies for CD69 (BioLegend). In parallel, anti‐CD19 CAR expression was measured using Flow cytometry. First, anti‐CD19 CAR expression was measured with commercial bio‐sCD19‐Fc (ACROBiosystems), followed by staining with secondary APC‐conjugated SA antibody (BioLegend). Anti‐CD19 CAR expression was measured with sCD19‐SA, followed by a secondary PE‐conjugated anti‐SA antibody (BioLegend), and anti‐CD19 CAR expression was directly measured with FITC‐sCD19‐SA. To assess cytokines produced by CAR‐T cells, cells were incubated in 96‐well U‐bottom plates at 105 cells/100 μl media/well for 24 h in the presence of 60 μg/ml sCD19‐SA with 5 μg/ml Brefeldin A (BioLegend), and the hGM‐CSF‐SA fusion protein (prepared in our laboratory) was added to the medium alone as a negative control. Before permeabilization with ice‐cold methanol, the cells were fixed in 1.5% formaldehyde and then incubated with antibodies against FITC‐TNF‐α, PE‐IFN‐γ, and APC‐IL‐2 (all from BioLegend) for flow cytometric analysis. A total of 104 cells were counted by flow cytometry for each experiment.
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2

Murine NK Cell Functional Analysis

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Nr-CWS was supplied by Greatest Biopharma Limited Company (purity>98%). Fluorescein conjugated anti-mouse antibodies APC-NK1.1, FITC-NK1.1, APC/Cy7-CD3ε, PE/Cy7-CD3ε, APC-CD4, PE-CD8α, PerCP/Cy5.5-CD11b, PE-CD27, FITC-TNF-α, and PerCP/Cy5.5-IFN-γ from BioLegend, and PerCP/Cy5.5-CD69, FITC-FasL, PE-TRAIL, PE-Perforin, and FITC-Granzyme-B from eBioscience were used in this study. TUNEL assay kit and MTS Cell proliferation, cytotoxicity or chemosensitivity assays kit (cat # 3580) were obtained from Promega. The LEGENDplex™ Multiplex mouse cytokine kit was provided by BioLegend. EasySep™ mouse NK cell isolation kit was from STEMCELL Technologies Inc. Recombinant murine IL-2 was from PeproTech Inc.
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3

Flow Cytometric Analysis of Immune Cell Subsets

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Cells were washed once in FACS buffer (PBS containing 0.1% BSA) before blocking with anti-FcγRII/FcγRIII (2.4G2, BD Pharmingen). Staining of surface molecules (all Biolegend) was performed on ice using FITC-conjugated CD4 (RM4-5), CD8α (53-6.7), and CD90.1 (OX-7); PECy7-conjugated CD44 (IM7); PE-conjugated α4β7 (LPAM-1, DATK32), CD4 (RM4-5), CD8α (53-6.7), CD62L (MEL-14), CD44 and CD25 (PC61); APC conjugated CD90.1 (OX-7). Intracellular Foxp3 (FJK-16s, APC-conjugated; eBioscience), NFATc1 (anti-NFATc1 PE 7A6, Biolegend), IRF4 (3E4, APC or PB-conjugated; Biolegend) staining was performed using the Foxp3 staining kit (eBioscience) according to the manufacturer’s instructions. Antibodies (all Biolegend) for intracellular cytokine staining were APC-IFN-γ (XMG1.2), FITC-TNF-α (MP6-XT22) and PE-IL-2 (JES6-5H4). Cytokine detection was performed after a 6 h in vitro restimulation with 12-O-tetradecanoylphorbol-13-acetate (TPA; 10 ng/mL, Sigma) plus ionomycin (5 nM, Merck Biosciences) in the presence of GolgiStop and GolgiPlug (both BD Pharmingen) using the IC Fixation Buffer kit (eBioscience). Viable cells were detected with the Zombie Aqua™ Fixable Viability Kit (Biolegend). Data were acquired on a FACSCanto II (BD Biosciences) flow cytometer and analyzed with FlowJo software (Tree Star).
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4

Quantifying Virus-Specific CD8 T Cells

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Purified PBMCs were thawed and rested overnight at 37°C and 5% carbon dioxide in complete RPMI medium. After overnight rest, PBMCs were stimulated for 6 hours with 2μg/mL HIV-1 Gag pools or cytomegalovirus (CMV) pp65 (JPT Peptide Technologies, Berlin, Germany) or with 0·005% dimethyl sulphoxide (DMSO) as a negative control in the presence of αCD28/αCD49d co-stim antibodies (1 μg ml–1) GolgiStop (containing Monensin, 2 μmol/L), GolgiPlug (containing brefeldin A, 10 μg ml–1) (BD Biosciences) and anti-CD107a APC-H7 antibody (BD Biosciences). After stimulation, virus-specific CD8 T cells were identified by interferon γ (IFN-γ) and Tumour necrosis factor (TNF-α) production. Briefly, cells were surface stained and then fixed and permeabilized (CytoFix/CytoPerm; BD Biosciences) followed by intracellular cytokine staining with IFN-γ PE-Cy7 (BD Biosciences), TNF-α FITC (BioLegend). Samples were acquired on a BD Fortessa X20 using BD FACSDiva8.0 (BD Bioscience) and data analysed using FlowJo 10 (TreeStar).
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5

Comprehensive Immune Cell Profiling

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Fresh PBMCs were stained with anti-CD3-APC-Cy7, CD8-APC, CD45RA-PE-Cy5, CCR7-PE-Cy7, PD-1-Pacific Blue, IL-7Rα-FITC, CD27-PE, CD28-PE, CTLA4-PE, CX3CR1-PE antibodies or isotype control (all from BioLegend, San Diego, CA). PBMCs that had been stimulated with PMA/ionomycin were stained with anti-CD3-APC-Cy7, CD8-APC, CD45RAPE-Cy5 and CCR7-PE-Cy7 antibodies followed by fixation, permeabilization (Cytofix/Cytoperm Kit, BD Biosciences) and staining with anti-IFNγ-PE, TNF-α-FITC or IL-13-PE antibodies (BioLegend).14 (link) Stained cells were analyzed on an LSRII® flow cytometer (BD Biosciences). Collected data were analyzed using FlowJo software (Tree Star, Ashland, OR).
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6

Single-Cell Immune Profiling of Mouse Spleens and Tumors

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Mice were euthanised at the end of the study; single-cell suspensions were prepared from the spleens and tumours as described in our previous study.18 (link) Spleen cells and tumour cells were stained with respective stain cocktails. Anti-mouse CD11b-PE (phycoerythrin) (101208), Ly6C-APC (allophycocyanin) (128015), Ly6G-FITC (fluorescein isothiocyanate) (127605), Gr1-PE/Cy7 (108416), CD11C-Pacific Blue (117321), major histocompatibility complex II (MHCII)-AF700 (107622), CD3-PerCP/Cy5.5 (100217), CD4-PE/Cy5.5 (100410), CD8-BV510 (100751), interleukin (IL)-2-PE (503808), IFN-γ-APC (505809), tumour necrosis factor (TNF)-α-FITC (506304), and Granzyme B-PE/Cy7 (372213) were purchased from Bio Legend (San Diego, CA). Cells were acquired through BD LSRII flow cytometer (BD Biosciences, San Jose, CA, USA). Flow cytometric analysis was performed by using the Flow Jo software (Tree Star Inc., Ashland, OR, USA). For co-cultures experiments, cells were sorted by using BD FACS ARIA III (BD Biosciences, San Jose, CA, USA).
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7

Multiparametric Flow Cytometry Analysis of T Cell Subsets

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CD1a-PE, CD1b-PE, CD1c-FITC, B220-PerCPCy5.5, F4/80-APC, CD11c- BV421, CD8-BV510, CD4-PerCPCy5.5, IFN-γ-APC, IL-17-PE, Granzyme B-BV421, and TNF-α-FITC antibodies were purchased from BioLegend (San Diego, CA). TCR-β-BV421, anti-Vβ3 and 4-PE, and anti-Vβ5.1/5.2-APC were obtained from BD biosciences (San Jose, CA). For flow cytometry, single cell suspensions from organs were incubated with 2.4G2 FcR blocking antibody for 10 minutes and then stained in HBSS-2% FBS containing 50 μg/mL gentamicin. Samples were run on the FACS Canto II flow cytometer (BD Biosciences, San Jose, CA). Analysis of flow cytometry data was performed on FlowJo software (Tree Star, Inc). S12 Fig shows the gating strategies employed for the FACS plots of group 1 CD1-restricted T cells in the polyclonal setting in Fig 3 and group 1 CD1-restricted T cell line functional assays in Fig 5.
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8

Multicolor Flow Cytometry of PBMC

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We isolated peripheral blood mononuclear cells (PBMC) from peripheral blood by Ficoll gradient and we stored them in liquid nitrogen for batched analysis. For multicolor flow cytometry analyses, we used the following monoclonal antibodies: from Becton Dickinson (BD, Franklin Lakes, NJ), CD3-FITC, CD3-PerCP-Cy5.5, CD4-APC-Cy7, CD8-BV510, CD45RO-FITC, CD45RA-APC, CD45RA-APC-Cy7, CD71-PE, IgD-PerCP-Cy5.5, CD25-APC-Cy7, CD138-BV421, CCR4-PE, CD27-PE, CD95-BV421, CD28-BV421, TIM3-BV421, CCR6-BV421, CCR7-AF700, CXCR3-PE, IL-2-PE, IL-17-BV786, and IFN-γ-PE-Cy7; from Biolegend (San Diego, CA), CD19-BV510, CD56-FITC, CD27-APC, CD127-FITC, CD57-PerCp-Cy5.5, PD-1-APC-Cy7, CXCR5-FITC, LAG3-APC, IL-10-PerCP-Cy5.5, and TNF-α-FITC. From eBioscience (San Diego, CA), CD4-PE-Cy7, CD21-PE, and CD24-APC-Cy7 were used. From Miltenyi Biotec (Auburn, CA), CD25-APC and anti-KLRG1-PE were used. From Beckman Coulter (Indianapolis, IN), CD38-PE-Cy7 was used.
We performed intracellular staining for IL-2, IL-4, IL-17, IFN-g, and TNF-a together with extracellular markers for CD4+, CD8+, and CD19+. Cells were fixed and permeabilized using Intracellular Fixation and Permeabilization Buffer Set (eBioscience) according to the manufacturer’s instructions.
Data were acquired (> 1 × 106 events) on a 3-laser FACSLyric flow cytometer (BD Biosciences) and analyzed with FlowJo® software.
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9

Multiparametric Flow Cytometry of Immune Cells

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The following fluorochrome-conjugated antibodies were used in this study: CD14 BV510, CD19 BV510, CD3 APC Fire 750 or CD3 BV605, CD4 PE/Dazzle 594, or CD4 APC Fire 750, CD8 BV421, CCR5 PE/Dazzle 594, CD56 PeCy7 (Biolegend) for surface antigens; and IFN-γ PeCy7, TNF-α FITC (Biolegend) and IL-2 PercP eFluor710 (eBioscience), for intracellular staining. PBMC were washed in PBS, and surface stained at 4°C for 20 min with saturating concentrations of different combinations of antibodies in the presence of fixable live/dead stain (Invitrogen). Cells were then fixed and permeabilized for detection of intracellular antigens. Cells were acquired on a BD Fortessa X20 using BD FACSDiva8.0 (BD Bioscience) and analysed using FlowJo 10 (Tree Star). Stochastic neighbor embedding (SNE) analysis was performed using the mrc.cytobank platform.
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