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7 protocols using anti t bet

1

Immunization and T-cell Response Analysis

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For protein immunization, C57BL/6 mice were immunized with Ag85B or MAP1889c (50 μg/mice) via intravenous injection administered three times at 2-week intervals. Two weeks after the final immunization, the spleens were isolated from the mice. The single-cell suspensions were then filtered through a 40-μm cell nylon mesh cell strainer, treated with red blood cell lysis buffer (Sigma) for 5 min, and washed twice with RPMI 1640 medium supplemented with 2% FBS. Single-cell suspensions of the spleen of immunized mice were stimulated with Ag85B (10 μg/mL) or MAP1889c (10 μg/mL) for 12 h at 37 °C in the presence of GolgiStop (BD Biosciences). The cells were first blocked with Fc Block (anti-CD16/32; eBioscience) for 15 min at 4 °C and then stained with fluorochrome-conjugated anti-CD4 or anti-CD8 Ab (BD Biosciences) for 30 min at 4 °C. Cells stained with the appropriate isotype-matched immunoglobulins were used as a negative control. The cells were fixed and permeabilized using a Cytofix/Cytoperm kit (BD Biosciences) according to the manufacturer’s instructions. Intracellular anti-IL-10, anti-T-bet, or anti-GATA-3 (BD Biosciences) levels were detected with fluorescein-conjugated antibodies in permeation buffer. Then, the samples were detected by flow cytometry.
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2

Multiparametric Flow Cytometry Analysis

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The cells were preincubated for 20 min with anti-CD16/32 (2.4G2, Fc block from BioXCell) and stained for viability with LIVE/DEAD® (Invitrogen, Carlsbad, CA) for 20 min on ice. Cells were surface stained for flow cytometry with the combination of the following antibodies (eBioscience or Biolegend): Anti-CD45 (104), anti-CD3 (145-2C11), anti-Thy1.2 (30-H12), anti-B220 (RA3-6B2), anti-Ter-119 (TER119), anti-Gr-1 (RB6-8C5), anti-CD11c (N418), anti-CD5 (53-7.3), anti-Eomes (Dan11mag), anti-T-bet (4B10), anti-RORγt (Q31-378, BD Pharmingen), anti-IFNγ (XMG1.2), anti-IL-17a (TC11-18H10.1), anti-Ly6G (1A8), anti-CD11b (M1/70), anti-CD64 (X54-5/7.1), anti-CD103 (2E7), anti-MHCII (M5/114.15.2). For intracellular cytokine staining was cells (1 x 106 cells) were restimulated for 4 hours at 37°C with PMA (50 ng/ml) and ionomycin (500 nM) in the presence of brefeldin A (5 μg/ml) (all from Sigma-Aldrich, St. Louis MO) and fixed and permeabilized using fixation and permeabilization solution (eBiosciences). All cells were analyzed on either a FACS Celesta or LSR II (BD Biosciences) and analyzed with FlowJo software (FlowJo LLC).
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3

T Cell Differentiation Assay

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Naïve CD4+CD25- T cells were differentiated to the different effector subsets as detailed in Supplemental Experimental Procedures. For proliferation assays, cells were labeled Cell Violet (1 μM) and activated with anti-CD3/CD28 or differentiated as indicated. For intracellular staining of transcription factors, cells were differentiated during 3 days, collected with 5 mM EDTA in PBS, fixed, permeabilized and stained with anti-RORγT and anti-T-bet (BD biosciences). For intracellular cytokine staining, cells were restimulated for 4 hr with PMA and ionomycin in the presence of brefeldin, permeabilized with 0.5% saponin and stained with anti-CD4, anti-IFN-γ, anti-IL-17 and anti-Foxp3. Data were acquired on a FACSCanto flow cytometer (BD Bioscience) and analyzed using the FLOWJO software (Tree Star).
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4

Multiparametric Profiling of T Cell Subsets

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eFluor660-anti–IL-21, Alexa Fluor 488–anti–IL-10, PerCP-Cy5.5-anti–IFN-γ, FITC-anti-CD45RA, PE-anti-ICOS, and anti-Tbet, and biotin–PD-1 were from eBioscience. Alexa Fluor 488–anti-GATA3, Alexa Fluor 647–anti-CXCR5, anti-pSTAT4, anti-pSTAT5, anti-pSTAT6, APC-anti-CD10, APC-Cy7-anti-CD4, BV605-anti-IgG, BV421-CD40L, BV711-anti–IL-2, PE-anti-pSTAT1, anti-RORγt, and Bcl-6, PE-Cy7-anti-CD25, and anti-CD27, PerCP-Cy5.5-anti-CD127, anti-pSTAT3, and anti-Tbet, SA-PerCpCy5.5, and IFN-γ were obtained from BD. Pacific Blue–anti-CD20 and SA-BV605 were purchased from BioLegend. Recombinant human IL-12 was purchased from R&D Systems. TGF-β, IL-1β, IL-6, IL-21, and IL-23 were obtained from PeproTech. PGE2 was purchased from Sigma-Aldrich. Human IL-4 and IL-10 were provided by R. de Waal Malefyt (DNAX Research Institute, Palo Alto, CA).
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5

Epigenetic Profiling by ChIP-seq and RNA-seq

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ChIP-seq assays were performed as described previously 3 ,18 . In brief, cells for ChIP-seq were fixed for 10 minutes in 1% formaldehyde and sonicated and chromatin immunoprecipitation was performed with anti-H3K4me1(ab8895, Abcam), anti-H3K4me2 (ab32356, Abcam), anti-H3K4me3 (17–614, Millipore), anti-H3K9me3 (ab8898, Abcam), anti-H3K27ac (ab4729, Abcam), anti-H3K27me3 (07–449, Millipore), anti-MLL4 19 ,20 , anti-GATA3 (558686, BD bioscience), anti-T-bet (561263, BD bioscience). DNA was end-repaired using an End-It DNA-Repair kit (Epicentre), and was indexed, amplified and sequenced on an Illumina HiSeq-2500. RNA-seq libraries using poly-A RNA isolated from both the WT and MLL4 KO cells were prepared as previous described 21 and sequenced by Illumina HiSeq-2500.
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6

Cytokine and Transcription Factor Analysis in Immune Cells

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For measurement of intracellular cytokine expression, cells were isolated ex vivo and stimulated with 50 ng/ml PMA and 500 ng/ml ionomycin, in the presence of GolgiStop (BD Biosciences) for 3 h. Dead cells were excluded by Fixable Viability Dye eFluor 450 (eBioscience). Cells were stained with antibodies to surface antigens, and then fixed and permeabilized with the Cytofix/Cytoperm kit (BD Biosciences), followed by staining with anti-IL-5 (Biolegend) and anti-IL-13 (eBioscience).
For analysis of transcription factor expression, cells were stained with antibodies to surface antigens, then fixed and permeabilized with the Foxp3/Transcription Factor Staining Buffer Set (eBioscience) according to the manufacturer’s instructions, and stained with anti-GATA3 (eBioscience), anti-RORγt, anti-T-bet (BD Biosciences), or anti-Ki-67 (eBioscience).
For measurement of intracellular HIF1α, Lin bone marrow cells were cultured in complete media with 10 ng/ml IL-7 (Peprotech) and 10 ng/ml IL-33 (R&D Systems) for 4 days. Cells were collected and stained with antibodies to surface antigens, fixed and permeabilized with the Foxp3/Transcription Factor Staining Buffer Set (eBioscience) according to the manufacturer’s instructions, and then stained with anti-HIF1α (R&D Systems).
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7

Multiparametric Analysis of MAIT Cells

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Cells were stained with fixable viability dye (eBioscience-Thermo Fisher Scientific, Bleiswijk, The Netherlands) and then with the following antibodies for surface staining: anti-TCRVα7.2, anti-CD161, anti-CD3, anti-ST2, anti-CD4 and anti-CD8 (SONY biotechnology, Weybridge, United Kingdom) (eBiosciences-Thermo Fisher Scientific) (Biolegend, Amsterdam, The Netherlands). MAIT cells were identified as TCRVα7.2+CD161+ or MR1 5-OP-RU tetramer+ cells. MR1 6-FP tetramer+ was used as negative control (NIH Tetramer Facility, Atlanta, GA, USA) (Figure S1). For intracellular cytokine staining, cells were fixed in 4% paraformaldehyde, washed, and permeabilized with 0.5% saponin (Sigma-Aldrich), and then incubated with anti-IFNγ, anti-TNFα, anti-Granzyme B or isotype controls (eBiosciences-Thermo Fisher Scientific, SONY biotechnology or BioLegend). In some experiments, MAIT cells were stained intracellularly with anti-Tbet (BD Biosciences, Grenoble, France) and anti-PLZF (R&D Systems) antibodies using a transcription factor buffer set (BD Biosciences). Events were acquired on a FACS LSR Fortessa (BD Biosciences) and analyzed using FlowJo software v10.7.1 (Becton, Dickinson and Company, Ashland, OR, USA).
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