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6 protocols using eomes dan11mag

1

Comprehensive Immune Profile of T Cells

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Surface staining was performed for 30 min and with tetramer for 90 min at 4°C in PBS supplemented with 2% FCS and 0.01% azide (FACS buffer) using the following antibodies: anti-CD8α (53-6.7), CD127 (eBioSB/199), LAG-3 (C9B7W), and KLRG-1 (2F1; all eBioscience); anti–PD-1 (RMP1-30; BioLegend); gp276–286 tetramer (TCMetrix); and anti-CD4 (GK1.5), CD45.1 (A20), and CD45.2 (clone 104), obtained from or custom purified by Bio X Cell and coupled to Pacific blue, Alexa Fluor 647, or FITC using labeling reagents from Invitrogen. Cells were washed twice and fixed in PBS supplemented with 1% formaldehyde, 2% glucose, and 0.03% azide for 20 min. Then, cells were washed again and resuspended in FACS buffer. For intracellular cytokine staining, cells were fixed and permeabilized using the Cytofix/Cytoperm kit (BD) and stained with anti–IFN-γ (XMG1.2), TNF (MP6-XT22; both from eBioscience), or granzyme B (GB12; Invitrogen). T-bet and Eomes staining was performed with a transcription factor staining kit (eBioscience) and stained with Eomes (Dan11mag) and T-bet (eBio4B10; both from eBioscience).
For flow cytometry sorting, living cells were stained in 10% FCS RPMI media and sorted on a FACSAria instrument (BD).
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2

Characterization of CD8+ T Cell Subsets

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Cells were incubated with αCD16/32 (clone 2.4G2; hybridoma supernatant) and plated on U-bottom 96-well plates at ≤ 3 × 106 cells/well in complete RPMI. Where indicated, cells were stained with Kb-SIINFEKL tetramer APC (NIH tetramer core) at 37°C for 30 min in the presence of αCD8α (53–6.7; Biolegend). For live-dead and surface staining, cells were washed with media, and stained in media for 20 min at RT with Fixable Viability Dye 780 (eBioscience) and surface antibodies for CD19 (6D5, Biolegend), CD8α (53–6.7, Biolegend), CD44 (IM-7; Tonbo), CD127 (A7R34, Tonbo), KLRG1 (2F1/KLRG1, Biolegend), CD45.1 (A20, Biolegend), CD45.2 (104, Biolegend), CD122 (TM-b1, Biolegend). After wash with RPMI, cells were fixed and permeabilized for 45 min at RT in Foxp3/Transcription Factor 1× Fix/Perm solution (Tonbo), followed by wash with 1× Flow Cytometry Perm Buffer (Tonbo) and intracellular staining for 45 min at RT with intracellular antibodies, including TCF1 (C63D9; Cell Signaling Technology), FOXO1 (C29H4, Cell Signaling Technology), T-bet (4B10, Biolegend), EOMES (Dan11mag; eBioscience). The cells were washed twice and resuspended in 1× Flow Cytometry Perm Buffer (Tonbo). Flow cytometry data was acquired on a four-laser (405, 488, 561, 638 nm) CytoFlex S (Beckman Coulter) and analyzed using FlowJo software (BD Biosciences).
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3

Multiparameter Flow Cytometry Analysis

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Antibody staining of tumor cell and splenocyte suspensions for flow cytometry analysis was performed following the antibody manufacturer's recommendations. Fluorophore-conjugated antibodies to NK1.1 (PK136), CD8a (53–6.7), CD4 (RM4–5), CD183 (CXCR3–173), CD25 (PC61), CD45 (30-F11), CD44 (IM7), CD69 (H1.2F3), and FoxP3 (FJk-16 s) were purchased from Biolegend, and the antibody to Ki-67 (MOPC-21) was purchased from BD Pharmingen. Viability Dye eFluor 455 (UV) and antibodies to CD62L (L-selectin) (MEL-14), T-bet (4B10), and EOMES (Dan11mag) were purchased from eBiosciences.
Cells were blocked with anti-CD16/CD32 (FcγRIII/FcγRII, 2.4G2) at a 1:25 dilution for 20 min, incubated with surface marker antibodies for 30 min on ice, stained with fixable viability dye for 30 min at 4 °C, and then permeabilized with BD Cytofix/Cytoperm buffer before intracellular labeling antibodies (Foxp3, T-bet, and Ki-67) were added for an overnight incubation at 4 °C. Cells were analyzed on a BD LSR II flow cytometer according to the manufacturer's instructions. Flow cytometry analysis was performed using BD FACSDiva® software (V8). Cellular events were first gated by forward and side scatter characteristics and then by viability (Supplementary Fig. S1). Tumor and splenic cells were gated on immune cell subpopulations as described in the figure legends.
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4

Comprehensive Immune Cell Phenotyping

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Tissues were processed, single cell suspensions obtained, and cells were stained as described (Wherry et al., 2003). Cells were stained with LIVE/DEAD cell stain (Invitrogen) and with antibodies targeting KLRG1 (2F1/KLRG1, Biolegend), CD127 (A7R34, Biolegend), CD8 (53-6.7, Biolegend), CD44 (IM7, Biolegend), CD45.1 (A20, Biolegend), CD45.2 (104, Biolegend), CD62L (MEL-14, Biolegend), CD27 (LG.7F9, Biolegend), CD122 (TM-b1, eBioscience), CXCR3 (CXCR3-173, Biolegend), Bcl-2 (A19-3, BD PharMingen), Bcl-xL (H-5, Santa Cruz), Bcl-6 (K112-91, BD PharMingen), Eomes (Dan11mag, eBioscience), Ki-67 (16A8, BioLegend), Bim (C34C5, Cell Signaling Transduction), and MHC class I Dbgp33–41 tetramer (NIH tetramer core). Intracellular cytokine staining was performed after 5 hrs ex vivo stimulation with gp33–41 peptide in the presence of GolgiPlug (BD), GolgiStop (BD) and CD107a (1D4B, Biolegend). After stimulation, cells were stained with surface antibodies, following fixation with Fixation/Permeabilization Buffer (eBioscience) and then stained with intracellular antibodies for TNF (MP6-XT22, Biolegend), IFN-γ (XMG1.2, BD PharMingen), GrzmB (GRB17, Life Technologies) and MIP-1α (IC450P, R&D System) using Permeabilization Wash Buffer (eBioscience) according to manufacturer’s instructions. Cells were analyzed with LSRII (BD Biosciences) and FlowJo software (Treestar).
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5

Comprehensive Immune Profiling of Colon Tissue

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Single-cell suspensions were stained with the following antibodies: TCRβ (H57-597), NKp46 (29A1.4), NK1.1 (PK136) and fixable viability dye from eBioscience (San Diego, CA, USA); and CD4 (GK1.5), CD8 (53-6.7), CD19 (ID3), CD3ε (145-2C11), CD45 (30-F11), CD45.2 (104), CD90.2 (30-H12) and CD49a (Ha31/8) from BD Biosciences (Franklin Lakes, NJ, USA). Fixation and intracellular staining were performed using the Transcription Factor Staining Buffer Set (eBioscience) and antibodies against GATA-3 (TWAJ, eBioscience), RORγt (Q31-378, BD Biosciences) and EOMES (Dan11mag, eBioscience). Cytokine expression was determined by restimulation of cells isolated by digestion from the colon tissue in the presence of 100 ng/mL phorbol-12-myristate-13-acetate (PMA), 100 ng/mL ionomycin and 10μg/mL GolgiPlug™ and GolgiStop™ (BD Biosciences) in complete RPMI-1640 media (containing 10% heat-inactivated FCS, 1 mM L-glutamine, 100 U/mL penicillin, 100 μg/mL streptomycin and 50 µM β-mercaptoethanol) for 4 h. Cells were then fixed and stained for intracellular cytokines IFN-γ (XMG1.2, BD Pharmigen), TNF-α (Mab11, BD Pharmigen), IL-5 (TRFK5, eBioscience), IL-13 (eBio13A, eBioscience), IL-17A (TC11-18H10.1, BioLegend) and IL-22 (IL22JOP, eBioscience). Cells were analysed using a Fortessa X20 (BD Biosciences) and FlowJo software (Ashland, OR, USA) was used for the analysis.
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6

Intracellular Staining of PLZF and T-bet

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Single-cell suspensions from tissues were prepared. APC-conjugated CD1d-PBS-57 loaded and unloaded. Tetramers were obtained from the tetramer facility of the US National Institutes of Health. PLZF staining was done as previously described (Savage et al., 2008 (link)). Cells were stained for surface markers first, washed, and then fixed with the permeabilization and fixation buffer (Foxp3 Staining Buffer Set; eBioscience). Intracellular PLZF was detected with 2 µg/ml mouse monoclonal antibody D-9 (Santa Cruz Biotechnology, Inc.) and FITC-conjugated rat anti–mouse IgG1 (BD). Cells were stained for 1 h with Eomes (Dan11mag; eBioscience), T-bet (4B10; eBioscience) followed by secondary antibody staining in Foxp3 Staining Buffer Set (eBioscience). Data were analyzed by FlowJo (Tree Star).
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