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10 protocols using cd14 pacific blue

1

Isolation of SARS-CoV-2 RBD-Specific B Cells

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RBD-specific single B cells were sorted as previously described [29 (link)]. In brief, PBMCs from infected individuals were collected and incubated with an antibody cocktail and a His-tagged RBD protein for identification of RBD-specific B cells. The cocktail consisted of the Zombie viability dye (Biolegend), CD19-Percp-Cy5.5, CD3-Pacific Blue, CD14-Pacific Blue, CD56-Pacific Blue, IgM-Pacific Blue, IgD-Pacific Blue, IgG-PE, CD27-PE-Cy7 (BD Biosciences) and the recombinant RBD-His described above. Two consecutive staining steps were conducted: the first one used an antibody and RBD cocktail incubation of 30 min at 4 °C; the second staining involved staining with anti-His-APC and anti-His-FITC antibodies (Abcam) at 4 °C for 30 min to detect the His tag of the RBD. The stained cells were washed and resuspended in PBS containing 2% FBS before being strained through a 70-μm cell mesh filter (BD Biosciences). RBD-specific single B cells were gated as CD19 + CD27 + CD3-CD14-CD56-IgM-IgD-IgG + RBD+ and sorted into 96-well PCR plates containing 10 μL of RNAase-inhibiting RT–PCR catch buffer (1M Tris-HCl pH 8.0, RNase inhibitor, DEPC-treated water). Plates were then snap-frozen on dry ice and stored at −80 °C until the reverse transcription reaction.
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2

PBMC Isolation, Stimulation, and Intracellular Signaling

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PBMCs from healthy controls and patients were isolated from whole blood by Ficoll-Hypaque density centrifugation. Cells were plated at a density of 1 × 106 cells/well (PBMCs) or 1 × 105 cells/well (AMLs) in 100 μL RPMI supplemented with 10% FBS in 96-well V-bottomed plates. PBMCs were left unstimulated or were stimulated with 5 ng/mL GM-CSF or 100 ng/mL IL-3 (#130–093-908, Miltenyi Biotec) for 15 minutes at 37°C, before fixation and permeabilization. Extracellular labeling was performed with CD14-Pacific Blue (#558121, BD Biosciences, 1:50) and CD4-FITC (#347413, BD Biosciences, 1:50). Cell viability was determined with the Aqua Dead Cell Stain Kit and STAT5 phosphorylation was assessed by intracellular staining with a p-STAT5 (pY694)-PE antibody (BD Biosciences). Samples were assessed on a Gallios flow cytometer and analyzed with FlowJo v.10.6.2. We tested for neutralizing auto-antibodies against GM-CSF, by stimulating control PBMCs in the presence of 10% plasma obtained from patients or controls.
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3

Phenotypic Assessment of MDSCs and Tregs

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Cryopreserved PBMCs from each patient were assayed for phenotypic markers consistent with MDSCs and natural Treg cells as previously described.23 (link) Briefly, PBMCs from each patient were suspended at a concentration of 1×107/mL in flow staining buffer (PBS plus 1% FBS). Cells were incubated with fluorochrome-labeled antibodies at 4°C. Specific antibodies include CD4-APC (Beckman Coulter), CD15 FITC (eBioscience), CD33 PE (BD Biosciences), HLA-DR PERCP-Cy5.5 (eBioscience), CD11b APC (BD Biosciences), and CD14 Pacific Blue (BD Biosciences). PBMCs were also labeled with the appropriate isotype control antibodies for each fluorochrome to use as negative controls. Cells were then washed with flow buffer, fixed with 1% formalin, and stored at 4°C until analysis. All samples were run on a BD LSR II flow cytometer, and were subsequently analyzed with FlowJo software (Tree Star Inc.). MDSCs were defined as cells positive for CD33, and lacking HLA-DR with subsets expressing CD15, CD14, and CD11b. Natural Treg cells were defined as CD4+CD25+FoxP3+ and assessed using the commercially available Human T-regulatory cell staining kit per manufacturer’s recommendations (BD Biosciences).
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4

Single HIV-1 Trimer-Specific B Cell Sorting

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Thawed PBMCs were stained with an antibody cocktail consisting of CD19-PE-Cy7, CD3-Alexa Fluor 700, CD14-Pacific Blue, CD8-BV510, IgM-PE-Cy5, IgG-FITC (all from BD Biosciences), CD20-ECD (Beckman), and BG505 Probe-APC (kindly provided by The Scripps Research Institute). The sorting probe BG505 was a biotin-labeled HIV-1BG505 GP140 trimer50 (link) conjugated with streptavidin-allophycocyanin (SA-APC) (Invitrogen). A LIVE/DEAD Fixable Dead Cell Stain Kit (Pacific Blue) (Invitrogen) was used to exclude dead cells. Antigen-specific single B cells were gated as CD19+CD20+CD3-CD14-CD8-IgM-IgG+BG505+ and sorted into a 96-well PCR plate containing lysis buffer. The sorted plate was snap-frozen on dry ice and stored at −80 °C9. Flow cytometric data were acquired on an Aria SORP flow cytometer (BD Biosciences) and analyzed with the software FlowJo (TreeStar).
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5

Flow Cytometry Analysis of IPSDM Cells

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Flow cytometry was used to characterise the IPSDM cell populations used in the experiments. Approximately 1 × 106 cells were resuspended in flow cytometry buffer (D-PBS, 2% BSA, 0.001% EDTA) supplemented with Human TruStain FcX (Biolegend) and incubated for 45 minutes on ice to block the Fc receptors. Next, cells were washed once and resuspended in buffer containing one of the antibodies or isotype control. After 1 hour, cells were washed three times with flow cytometry buffer and immediately measured on BD LSRFortessa cell analyser. The following antibodies (BD) were used (cat no): CD14-Pacific Blue (558121), CD32-FITC (552883), CD163-PE (556018), CD4-PE (561844), CD206-APC (550889) and PE isotype control (555749). The data were analysed using FlowJo. The raw data are available on figshare (doi: 10.6084/m9.figshare.1119735).
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6

Identification of SARS-CoV-2 Nucleoprotein-Specific B Cells

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PBMCs from the COVID-19 patient were collected and incubated with the LIVE/DEAD™ Fixable Dead Cell Stain reagent (Thermo Scientific) to exclude dead cells. Cells were then stained with His-tagged WT SARS-CoV-2 NP (Sino Biological) and the fluorescent-labeled antibodies including CD19-PE/Cy7, CD3-Pacific Blue, CD8-Pacific Blue, CD14-Pacific Blue, CD27-APC/Cy7, IgG-FITC (BD Biosciences), followed by incubated with APC- and PE- labeled His-specific antibodies (Abcam). NP-specific single B cells were gated as CD19 + CD3-CD8-CD14-CD27 + IgG + NP + and sorted into 96-well PCR plates containing lysis buffer (Invitrogen) using a FACSAriaII Flow Cytometer (BD Biosciences). Plates were then snap-frozen on dry ice and stored at − 80 °C until RT reaction.
For intracellular staining, 293 T cells transfected by NP expression vectors were fixed and permeabilized using Fixation/Permeabilization Solution Kit (BD Biosciences), stained with NP-specific mAbs (P301-F7 or P301-H5) or the polyclonal antibody (pAb) (Sino Biological), followed by staining with APC-conjugated secondary antibody (Life Technologies). After washing, cells were resuspended and subjected to acquisition with a FACSCalibur Flow Cytometer (BD Biosciences). Data were analyzed with FlowJo software V10.6 (BD Biosciences).
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7

Immunophenotyping of PD1 and PD-L1 Expression

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Cell surface expression of PD1 (CD279) on CD4+T cells, CD8+T cells, CD56+ NK cells and CD3+CD8+CD56+NKT cells, and PD-L1 (CD274) on CD138+ MM cells, CD14+ monocytes/macrophages, CD11b+CD14+HLA-DR+ antigen presenting cells (APCs), CD11b+CD14HLA-DR−/lowCD33+CD15+ nMDSC, and CD11b+CD14+HLA-DR−/low mMDSC was determined on PBMCs or BMMCs from MM patients or healthy donors by multiparameter flow cytometry analysis. Cells were stained with CD11b APCCy7, CD14 Pacific blue, HLA-DR PECy7, CD33 PECy5, and CD15 FITC conjugated MAbs (BD Biosciences, San Jose, CA) for MDSC; as well as CD138 APC for MM cells, and CD4 PE-Cy5, CD8 PE-Cy7, CD56 FITC for effector cells (BD Biosciences, San Jose, CA).
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8

Phenotypic Immune Profiling of PBMCs

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Cryopreserved PBMCs from each patient obtained at day 0 and day 56 were assayed for phenotypic markers consistent with NK cells, T lymphocytes, myeloid derived suppressor cells (MDSC) and T regulatory cells as previously described (26 (link), 32 (link)). Briefly, PBMC from each patient were suspended at a concentration of 1x107/mL in flow staining buffer (PBS containing 1% FBS). Cells were incubated with fluorochrome-labeled antibodies for one hour at 4°C. Specific antibodies include CD4-APC (Beckman Coulter), CD8-APC (Beckman Coulter), NKRD1 (Beckman Coulter), CD33-PE (BD Biosciences), HLA-DR PERCP-Cy5.5 (eBioscience), and CD14-Pacific Blue (BD Biosciences). PBMC were also labeled with the appropriate isotype control antibodies for each fluorochrome to use as negative controls. Cells were then washed with flow buffer, fixed with 1% formalin, and stored at 4°C until analysis. All samples were run on a BD LSR II flow cytometer, and were subsequently analyzed with FlowJo software (Tree Star, Inc.). Monocytic MDSC were defined as cells with a CD33+HLA-DRnegCD14+ phenotype. T regulatory cells were defined as CD4+CD25+FoxP3+ and assessed using the commercially available Human T regulatory cell staining kit per manufacturer’s recommendations (eBioscience).
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9

Intracellular Cytokine Staining Workflow

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Intracellular cytokine staining was performed as previously described(1) using the following markers: CD3-APCH7, CD107a PECy7, CD14-Pacific Blue, CD16-Pacific Blue, CD4-PECy5.5, IFN-γ-PerCPCy5.5, CD45RO-AF700, CD19-Pacific Blue (BD Biosciences, San Jose, CA), TNFα-AF647, CD8-BV570, CCR7-BV711 (BioLegend, San Diego, CA), granzyme B-PE Texas Red (Invitrogen), CD27-PECy5 (eBioscience, San Diego, CA) perforin-FITC(Abcam, Cambridge, UK). Prepared cells were acquired using an LSR II flow cytometer equipped with BD FACSDiva software (BD Biosciences). Acquired data was analyzed using the FlowJo software version 7.6.3 (Tree Star).
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10

Multiparameter Flow Cytometry and Multiplex Cytokine Assays

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Eighteen-parameter flow cytometry analysis was performed with an LSR II (BD Biosciences, San Jose, CA). CD3 H7 allophycocyanin (APC, BD Biosciences) or CD40 ligand (APC-eFluor 780, eBioscience), CD3 Qdot655, CD4 Cy5.5 phycoerythrin (PE, Invitrogen), CD8 Qd705 (Invitrogen), CD27 PC5 (Beckman Coulter), CD45RO ECD (Beckman Coulter), CD14 Pacific Blue (BD Biosciences), CD57 Qdot655 (BD Biosciences), IL-17 PE (eBioscience) or IL-10 PE (BD Biosciences), IL-17 fluorescein isothiocyanate (FITC, eBioscience) or IL-1β FITC (eBioscience), IL-22 APC (R&D Systems) or IL-2 APC (BD Biosciences), IFNγ Cy7PE (BD Biosciences) and TNF Alexa 680 (BD Biosciences) were used in two separate panels. The data were analyzed using FlowJo (Tree Star), PESTLE (Mario Roederer) and SPICE (Mario Roederer). The values reported are background-subtracted.
Multiplex cytokine assays were performed using a customized Bio-Plex Pro assay (Bio-Rad) according to the manufacturer’s instructions and analyzed on a Luminex 200 System. The following cytokines were measured: IL-1β, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, IL-12 (p70), IL-13, IL-15, IL-17, G-CSF, GM-CSF, IFNγ, MCP-1, MIP-1β and TNF.
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