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36 protocols using anti cd3 apc cy7

1

HIV-1 Co-receptor Expression and P-gp Activity

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To characterize the HIV-1 co-receptors surface expression and to establish correlation of different subsets of CD3+CD4+ T cells with P-gp activity, we used two different panels of antibodies and Rho123 as P-gp fluorescent substrate. After isolating the PBMCs from HIV-1-seronegative donors and HIV-1-infected subjects, cells were resuspended in RPMI 1640 and stained with Rho123 as described in the previous section. Cells were then stained with two panels of antibodies: (i) Rho123 (FL1 channel), anti-CD4-APC, anti-CXCR4-PE, anti-CCR5-PerCP-Cy5.5 and anti-CD3-APC-Cy7 (all from Becton Dickinson); and (ii) anti-CD4-APC, anti-CCR7-PerCP-Cy5.5, anti-CD45RA-PE-Cy7, anti-CD27-V450/Pacific Blue and anti-CD3-APC-Cy7 (Becton Dickinson). After washing the excess of antibodies, cells were run on a LSRII flow cytometer (Becton Dickinson) and results analysed by FlowJo Software (vX.0.7) and GraphPad Prism 6. Statistical analysis for each staining and graph are detailed in the figure legends.
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2

Multiparametric Flow Cytometry of T Cells

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CD4+ T cells were stained with anti-CD3-APC Cy7 (clone SK7; BD Pharmingen, San Jose, CA, USA), anti-CD4-PerCP (clone S3.5; Invitrogen eBioscience) along with anti-interferon-γ (IFN-γ)-FITC (clone 4S.B3; Invitrogen eBioscience; for intracellular staining), anti-FoxP3-PE (clone 150D/E4; Invitrogen eBioscience; for intracellular staining) and anti-IL-17A-APC (clone eBio64DEC17; Invitrogen eBioscience; for intracellular staining). CD8+ T cells were stained with anti-CD3-APC Cy7 (clone SK7; BD Pharmingen), anti-CD8-APC (clone 17D8; Invitrogen eBioscience) along with anti-perforin-PE (clone delta G9; Invitrogen eBioscience; for intracellular staining), anti-granzyme B-PE (clone GB11; Invitrogen eBioscience; for intracellular staining), or anti-Fas ligand (FasL, CD178)-PE (clone NOK-1; Invitrogen eBioscience; for surface staining), respectively. Acquisitions were performed using Cell Quest Pro Software (BD Biosciences Immunocytometry Systems, San Jose, CA, USA) in a FACS Aira II analyzer (BD Biosciences Immunocytometry Systems). Data were analyzed using FlowJo Software Version 8.4.2 for Windows (Tree Star, Ashland, OR, USA).
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3

Measuring IL-15R Expression on BMMCs

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To estimate the surface expression of IL-15R receptor complex (CD122, CD132, CD215), BMMC were washed first in PBS (without Mg2+/Ca2+) buffer containing 1% BSA and 0.06% NaN3, and then with glycine buffer (0.1 M, pH 3.0). In the next step BMMC were stained with antibodies anti-CD3-APC-Cy7, anti-CD4-PeCy7 (Becton Dickinson, San Diego, CA, USA), anti-CD122-FITC, anti-CD132-APC and anti-CD215-PE (R&D Systems). After the washing step, cells were incubated with 7-AAD to stain and exclude dead cells. Cells were acquired and analysed using FACSAria and Diva software (BD).
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4

Comprehensive TCR Repertoire Profiling

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T cell receptor (TCR) variable (V) chain expression of TCC was determined using flow cytometry after staining with a viability dye (Violet Live/Dead stain; Invitrogen), anti-CD3APC-Cy7, anti-CD4PerCP-Cy5.5 (Becton, Dickinson), anti-CD8PE-Cy7, and a panel of fluorescein isothiocyanate (FITC)-, PE-, and FITC-PE-conjugated MAbs covering approximately 70% of the known TCRV repertoire (IOTest Beta Mark MAb kit; Beckman Coulter).
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5

Flow Cytometric Analysis of Chemokine Receptors

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Agonist or inhibitor-treated cells were incubated with undiluted goat serum for 30 mins at 4°C, then washed in FACS buffer (1% BSA in PBS). Cells were resuspended with FACS buffer containing anti-CCR1-PE, anti-CD3-APC-Cy7, or anti-CD14-Pacific Blue (BD Biosciences Pharmingen, Palo Alto, CA), or anti-CCR2-PE antibody (R&D systems, Minneapolis, MN), and incubated at 4°C for 30 mins. After washing twice with FACS buffer, the cells were resuspended in FACS buffer, and analyzed using FACS Calibur, FACS Aria, or LSRII flow cytometers (BD Biosciences). A minimun of 10,000 gated cells were analyzed per sample for the relevant cell surface receptor expression. For quantification analysis of CCR1 and CCR2, the mean fluorescent intensities of CCR1-PE or CCR2-PE labeled cells were converted to the number of antibody bound receptors with Quantibrite PE calibration beads (Becton Dickinson, San Jose, CA) according to the manufacturer’s instructions.
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6

Comprehensive Immunophenotyping of T Cells

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Cells were stained with 7-AAD viability dye, anti-CD3 eFluor450, anti-CD4 PE-eFluor 647 (eBioscience), anti-CD4 electron coupled dye (Beckmann Coulter), anti-CD4 fluorescein isothiocyanate (FITC), anti-CD3 PE, anti-CD3 APC-Cy7, anti-CD8 PE, anti-CD8 APC-Cy7, anti-CD25 PECy7, anti-CD127 PE, and anti-CD27 FITC (BD), anti-CD45RA FITC, FOXP3 Alexa Fluor 647 (BioLegend) specific antibodies. FOXP3 intracellular staining was performed using FOXP3 staining buffers (eBioscience). Data were acquired using a fluorescence activated cell sorting (FACS)CantoII and analysed using FACSDiva software (BD) and Flojo software (Treestar).
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7

Multiparametric Flow Cytometry of PBMCs

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PBMC were thawed and rested overnight at 37°C in RPMI1640 supplemented with 10% heat-inactivated FCS, 100 U/ml penicillin, 100μg/ml streptomycin, and 2 mM glutamine (R10). The following day, the cells were stained with LIVE/DEAD Fixable Dead Cell Stain Kits (Invitrogen), washed and stained with the following antibodies: anti-CD3-APC-Cy7, anti-CD4-V450, anti-CD8-PE-Cy7, anti-CD45RA-APC (BD Biosience), and anti-CCR7-PE (e-BioScience). The cells were washed and fixed with 1% Formaldehyde in PBS. All data were collected on a BD LSR II flow cytometer (BD Biosience) and analyzed using FlowJo 8.7.7 (TreeStar).
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8

Immune Cell Profiling in Testes

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Immune cells in peripheral blood were collected and counts and phenotypes were analyzed by flow cytometry. The original data are reported in our previous studies (33 (link), 34 (link)). Interstitial cells in the testes were isolated as described previously (10 (link)). Briefly, testicular tissues were chopped and then incubated at 37°C with collagenase and DNase for 1 h. Tubule fragments were allowed to settle for 3 min, followed by interstitial cell recovery in PBS. Subsequently, the phenotypes of the interstitial cells were analyzed by multi-parameter flow cytometry. The anti-human flow cytometry antibodies cross-reactive with NPMs included anti-CD45-PE (557059, BD, USA), anti-CD3-APC-Cy7 (557757, BD), anti-CD20-FITC (302304, BioLegend, USA), anti-CD4-PerCP-Cy5.5 (317428, BioLegend), anti-CD8-PE-Cy7 (557746, BD), anti-Ki67-PE (51-36525X, BD), and anti-PD-1-PE (329906, BioLegend).
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9

Cytotoxic T Cell Activation Assay

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Clone cells were washed and left in fresh RPMI 1640 CM (5% AB serum) without IL-2 to rest for 5 hours or overnight before being stimulated with RL9 peptide pulsed K562-E (50μM, 20-24 hours at 27°C), K562-E-RL9 or K562-D-RL9 cells at a clone: K562 cell ratio of 1:3 for 1 hour, followed by addition of 5μg/ml Brefeldin A (Biolegend) and 5μg/ml GolgiStop (BD Biosciences) for an additional 8 hours at 37°C. For CD107 staining, anti-CD107a-BV421 and anti-CD107b-BV421 (Biolegend) antibodies were added at the beginning of the co-culture. After 9 hours incubation, cells were washed with PBS and stained with Live/Dead Fixable Aqua, anti-CD8-PerCP-Cy5.5 and anti-CD3-APC-Cy7 for 30 min at RT first, then fixed/permeabilized with Cytofix/Cytoperm 1x Solution (BD Biosciences) for 10 min at 4°C, and stained in Permwash 1x Solution (BD Biosciences) with anti-TNFα-PE, anti-IFN-γ–FITC and anti-CD137-BV650 (All BioLegend) for 30 min at RT. After being washed with PBS and fixed with 2% paraformaldehyde, samples were acquired using an LSR Fortessa (BD Biosciences) and analyzed using FlowJo software v10.3 (Tree Star). In the selected assays to determine HLA-E restriction, K562-E cells were pre-incubated with the VL9 canonical signal peptide (VMAPRTLVL, 50μM, 3 hours at 27°C) prior to addition of RL9 peptide.
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10

Phenotypic Analysis of T-cell Responses to Mycobacterial Infection

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PBMCs (2 × 105 cells) were stimulated with M. avium bacilli and M. intracellulare bacilli individually for 48 h and incubated with GolgiPlug (1 μL/mL; BD Pharmingen, San Diego, CA, USA) for the final 5 h of culture. Cells were measured by flow cytometry using a fluorescence activated cell sorter (FACS) (FACSVerse, BD Biosciences, San Jose, CA, USA) and anti-CD3-APC-Cy7, anti-CD4-FITC, anti-IFN-γ-PE, anti-IL-4-PE, anti-IL-17A-APC, anti-CD25-PE, anti-Foxp3-APC, anti-T-bet-APC, anti-GATA3-APC, and anti-RORγT-APC antibodies (BD Pharmingen, San Diego, CA, USA). The PD-1, CTLA-4, and TIM-3 were also stained with anti-PD-1-PE, anti-CTLA-4-APC, and anti-TIM-3- APC (BD Biosciences, San Diego, CA, USA). Data were analyzed using BD FACSuite software (BD Biosciences, San Jose, CA, USA). A gate was set on the lymphocytes using characteristic forward scatter and side scatter parameters followed by CD3+CD4+ T cells (Supplementary Figure S1).
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