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8 protocols using anti tnf α efluor 450

1

Comprehensive Phenotyping of Antigen-Specific T Cells

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We thawed PBMCs from cryovials and washed them as described above, and we seeded 2.5 × 106 cells/ml in RPMI 1640 with 10% FBS or 2% Phx. We stimulated PBMCs with 10 multiplicities of infection (MOIs) of strain 1100–2 fixed E. coli for 20 h and blocked extracellular transport with brefeldin A for a total of 4 h. We performed extracellular staining with fixable viability dye eFluor 780 (eBioscience), anti-CD3-BUV395 (BD Biosciences), anti-CD8-BV605 (BioLegend), anti-CD4-BV510 (BioLegend), anti-Vα7.2-PE-Cy7 (BioLegend), anti-LAG-3-BV786 (BioLegend), anti-CD25-BV650 (BioLegend), anti-PD-1-PerCPCy-5.5 (BioLegend), anti-CD161-PE/Dazzle-594 (BioLegend), anti-CD69-PE-Cy5 (Invitrogen), anti-CD161-allophycocyanin (BioLegend), and anti-human PE-MR1–5-OP-RU tetramer (NIH Tetramer Core Facility). The PBMCs were fixed and permeabilized using an Foxp3/transcription factor kit (eBioscience) and stained intracellularly with anti–granzyme B Alexa Fluor 700 (BioLegend), anti-TNF-α-eFluor-450 (Invitrogen), anti-IFN-α-FITC (BioLegend), and anti-T-bet-BV711 (BioLegend). We collected data using a five-laser LSRFortessa flow cytometer (BD Biosciences), and the flow data were analyzed using FlowJo software version 10 (BD Biosciences).
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2

Comprehensive Phenotyping of Antigen-Specific T Cells

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We thawed PBMCs from cryovials and washed them as described above, and we seeded 2.5 × 106 cells/ml in RPMI 1640 with 10% FBS or 2% Phx. We stimulated PBMCs with 10 multiplicities of infection (MOIs) of strain 1100–2 fixed E. coli for 20 h and blocked extracellular transport with brefeldin A for a total of 4 h. We performed extracellular staining with fixable viability dye eFluor 780 (eBioscience), anti-CD3-BUV395 (BD Biosciences), anti-CD8-BV605 (BioLegend), anti-CD4-BV510 (BioLegend), anti-Vα7.2-PE-Cy7 (BioLegend), anti-LAG-3-BV786 (BioLegend), anti-CD25-BV650 (BioLegend), anti-PD-1-PerCPCy-5.5 (BioLegend), anti-CD161-PE/Dazzle-594 (BioLegend), anti-CD69-PE-Cy5 (Invitrogen), anti-CD161-allophycocyanin (BioLegend), and anti-human PE-MR1–5-OP-RU tetramer (NIH Tetramer Core Facility). The PBMCs were fixed and permeabilized using an Foxp3/transcription factor kit (eBioscience) and stained intracellularly with anti–granzyme B Alexa Fluor 700 (BioLegend), anti-TNF-α-eFluor-450 (Invitrogen), anti-IFN-α-FITC (BioLegend), and anti-T-bet-BV711 (BioLegend). We collected data using a five-laser LSRFortessa flow cytometer (BD Biosciences), and the flow data were analyzed using FlowJo software version 10 (BD Biosciences).
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3

MAIT Cell Activation and Cytokine Production

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We cultured 2,000–5,000 MAIT cells from MAIT cells expanded in RPMI 1640 with 10% FBS or 2% Phx with 10,000–25,000 THP-1 cells to serve as APCs in RPMI with 10% FBS without cytokines overnight. We then stimulated the coculture of MAIT cells and THP-1 with 10 MOIs of strain 1100–2 fixed E. coli for 20 h and blocked extracellular transport with brefeldin A for a total of 4 h. For extracellular staining, we used Zombie ultraviolet fixable viability dye (BioLegend), anti-CD3-BUV395 (BD Biosciences), anti-CD8-BV605 (BioLegend), anti-CD4-BUV496 (BD Biosciences), anti-Vα7.2-PE-Cy7 (BioLegend), anti-LAG-3-BV786 (BioLegend), anti-CD69-BUV563 (BD Biosciences), anti-CD161-PE-Dazzle-594 (BioLegend), anti-TIM-3-BV421 (BioLegend), anti-CD25-BV650 (BD Biosciences), and anti-human PE-MR1–5-OP-RU tetramer (NIH Tetramer Core Facility). The cells were fixed and permeabilized using Foxp3/transcription factor kit (eBioscience) and stained intracellularly with anti-granzyme-B Alexa Fluor 700 (BioLegend), anti-TNF-α eFluor 450 (Invitrogen), and anti-IFN-γ-FITC (BioLegend). Sample data were acquired with a five-laser Cytek Aurora flow cytometer (Cytek) and analyzed using FlowJo software version 10 (BD Biosciences).
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4

MAIT Cell Activation and Cytokine Production

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We cultured 2,000–5,000 MAIT cells from MAIT cells expanded in RPMI 1640 with 10% FBS or 2% Phx with 10,000–25,000 THP-1 cells to serve as APCs in RPMI with 10% FBS without cytokines overnight. We then stimulated the coculture of MAIT cells and THP-1 with 10 MOIs of strain 1100–2 fixed E. coli for 20 h and blocked extracellular transport with brefeldin A for a total of 4 h. For extracellular staining, we used Zombie ultraviolet fixable viability dye (BioLegend), anti-CD3-BUV395 (BD Biosciences), anti-CD8-BV605 (BioLegend), anti-CD4-BUV496 (BD Biosciences), anti-Vα7.2-PE-Cy7 (BioLegend), anti-LAG-3-BV786 (BioLegend), anti-CD69-BUV563 (BD Biosciences), anti-CD161-PE-Dazzle-594 (BioLegend), anti-TIM-3-BV421 (BioLegend), anti-CD25-BV650 (BD Biosciences), and anti-human PE-MR1–5-OP-RU tetramer (NIH Tetramer Core Facility). The cells were fixed and permeabilized using Foxp3/transcription factor kit (eBioscience) and stained intracellularly with anti-granzyme-B Alexa Fluor 700 (BioLegend), anti-TNF-α eFluor 450 (Invitrogen), and anti-IFN-γ-FITC (BioLegend). Sample data were acquired with a five-laser Cytek Aurora flow cytometer (Cytek) and analyzed using FlowJo software version 10 (BD Biosciences).
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5

Multiparametric Immunophenotyping of Immune Cells

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For the evaluation of surface antigen expression the following monoclonal antibodies (mAbs) were used: CD3-APC-A700, CD19-APC-A700, CD56-ECD, PC7 and APC-A700, CD11b-FITC, CD33-PC7, HLA-DR-PE, CD14-ECD, CD45-KrO, CD66b-APC, CD15-APC (all Beckman Coulter), CD107a-eFLUOR660 (Invitrogen), CD275-, CD155-, CD85j-, Ceacam1-, CD39-APC (Miltenyi biotec). For intracellular evaluation the following mAbs were used: anti-IFN-γ-PE (BD, biosciences), anti-TNF-α-eFluor450 (Invitrogen). For MDSC immunostaining a custom Duraclone platform (Beckman Coulter) was used in order to standardize the protocol. After staining procedures cells were acquired at Cytoflex S and LX (Beckman Coulter) and analyzed with Cytexpert software (v2.2, Beckman Coulter), and FlowJo 10 (Starlab).
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6

Neoantigen-Specific T-cell Response Quantification

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The neoantigen-specific T-cell response was determined using intracellular cytokine staining (ICS) performed by FC detection and IFNγ ELIspot as previously described19 (link) For the FC analysis, the following antibodies were utilized according to different panels: anti-CD3-Alexafluor488 (cat. 53–0031-82, eBioscience), anti-CD3-PEefluor610 (cat. 61–0031-82, eBioscience), anti-CD4-PerCP-Cy5.5 (cat. 45–0042-82, eBioscience), anti-CD8-APCeFluor780 (cat 47–0081-82, eBioscience), anti-CD45-efluor450 (cat. 48–0451-82, eBioscience), anti-CD45-APC (cat. 559,864, BD), NK1.1-BV786 (cat. 740,853, Bio Legend), anti-CD11b-FITC (cat. 53,310, BD), anti-CD11c-SB645 (cat. 64–0114-82, Ebioscience), anti-LY6C-PE-Cy7 (cat. 560,593, BD), anti-LY6G-Alexafluor700 (cat. 561,236, BD), anti-IFN-γ-PE (cat. 12–7311-82, eBioscience), anti-TNF-α-PE-Cy7 (cat. 25–7321-82, eBioscience), anti-TNF-α-eFluor450 (cat. 48–7321-82, eBioscience FC was carried out with a Citoflex flow cytometer (Beckman Coulter) and data analyzed with Cytexpert software (Beckman Coulter). For the IFNγ ELIspot cells were plated at 4 × 105 and 2 × 105 cells/well in duplicate and spots were counted using an automated ELISPOT reader (Aelvis ELIspot reader, A.EL.VIS Gmbh, Germany).
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7

Splenocyte Phenotyping and Cytokine Analysis

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Isolated splenocytes were stimulated overnight with 10 µg/ml of Traspain in the presence of anti-CD154-PE and anti-CD107 PE-Cy7. Brefeldin A plus monensin was added to cultures during the last 6 h of incubation. Surface staining was performed with anti-CD3e-V500, anti-CD4-APC-H7 (BD), and anti-CD8α-Brilliant-Violet-650 (BioLegend). Cells were fixed with PFA 2%, permeabilized in 0.5% saponin, and stained using anti-IFN-γ-Brilliant-Violet-711 (BioLegend) and anti-TNF-α-eFluor450 (eBioscience) in accordance with the manufacturer’s instructions.
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8

Cytokine Profiling of T-Cell Responses

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Splenocytes were isolated and stimulated overnight with 10 μg/ml of Traspain or 10 μM of TEWETGQI peptide in the presence of anti-CD154 PE and anti-CD107 PE-Cy7. Brefeldin A plus monensin were added to cultures during the last 12 h of incubation. Dead cells were stained with LIVE/DEADTM Fixable Blue Dead Cell Stain Kit (Life Technologies). Surface staining was performed with anti-CD3e V500, anti-CD4-APC-H7 (BD), and anti-CD8α-Brilliant Violet 650 (BioLegend). Cells were fixed at RT with PFA 2%, permeabilized in 0.5% saponin and stained using anti-IFN-γ Brilliant Violet 711 (BioLegend) and anti-TNF-α eFluor450 (eBioscience) in accordance with the manufacturer's instructions.
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