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6 protocols using igd ia6 2

1

Immunophenotyping Peripheral Blood Subsets

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Fresh peripheral whole blood samples were immunophenotyped with predetermined optimal antibody concentrations to quantify T‐ and B‐cell peripheral subsets. The following anti‐human monoclonal antibodies (mAbs) were used to quantify B‐cell subsets: CD19 (HIB19), CD27 (L128) and immunoglobulin D (IgD) (IA6‐2) from BD Pharmingen (San Diego, CA, USA). For quantification of T‐cell subsets, we used the following mABs: CD3 (UCHT1), CD4 (RPA‐T4), CD8 (RPA‐T8), CD45RA (HI100), CD45RO (UCHL1), CD27 (L128) and CD31 (WM59), from BD Pharmingen. Cells were acquired in a FACSCalibur flow cytometer (Becton‐ Dickinson, San Jose, CA, USA), and data were analysed by the Flow Jo (TreeStar, USA) software. Gating strategies are shown (Supplementary figures 68), and results are expressed as absolute cell numbers.
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2

Comprehensive Immunophenotyping of PBMCs

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Peripheral blood mononuclear cells (PBMCs) were isolated through a Ficoll step gradient and stained for cell surface markers with the following fluorochrome-conjugated antibodies: CD38 (HIT-2, BD), IgD (IA6-2, BD), IgM (MHM-88, BioLegend), CD10 (HI10a, BD), CD19 (SJ25C1, BD), CD21 (B-ly4, BD), CD27 (0323, eBiosience), CD138 (B-B4, AbD SeroTec), IgG (SouthernBioTech #2043-09), IgA (G20-359, BD), CD3 (SK7, BD), CD28 (CD28.2, BD), FOXP3 (PCH101, eBioscience), CD8 (SK1, BD), CD4 (RPA-T4, eBioscience), γδ-TCR (B1.1, eBioscience), αβ-TCR (IP26, eBioscience), CD45RO (UCHL1, BD), CD45RA (HI100, BD), CD57 (NK-1, BD), CD31 (WM59, eBioscience), CD62L (DREG-56, BD), CD152/CTLA4 (BNI3, BD). Samples were acquired on a FACS-Canto II flow cytometer (BD) or on a Gallios flow cytometer (Beckman Coulter, Miami, FL) and analyzed using FlowJo version 7.6.5 analysis software (Treestar, Ashland, OR).
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3

Phenotyping Antigen-Specific B cells

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Freshly isolated peripheral blood mononuclear cells were stained first for viability with Live/dead Yellow (ThermoFisher) and then for markers with the following monoclonal antibodies: IgA (IS11–8E10, Miltenyi), IgD (IA6–2, BD), IgG (G18–145, BD), IgM (MHM-88, Biolegend), CD3 (SK7, BD), CD4 (RPA-T4, BD), CD8 (SK1, BD), CD14 (61D3, eBioscience), CD16 (CB16, eBioscience), CD19 (SJ25C1, BD), CD20 (2H7, BD), CD27 (O323, BioLegend or M-T271, BD), CD38 (HB7, BD), and CD71 (CY1G4, BioLegend. Antigen-specific B cells were detected by staining with RBD conjugated to Alexa Fluor 488 (Protein Labeling Kit, ThermoFisher). RBD was conjugated according to manufacturer’s instructions, with the following changes: protein was labeled at a concentration of 1mg/mL, and incubated for 30 minutes without the addition of bicarbonate. After staining, PBMCs were washed and then fixed for 30 minutes using 2% paraformaldehyde (ThermoFisher). Data were acquired on a BD FACSymphony A5 and analyzed using FlowJo 10.7.1 (BD).
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4

Comprehensive Immunophenotyping of PBMCs

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Peripheral blood mononuclear cells (PBMCs) were isolated through a Ficoll step gradient and stained for cell surface markers with the following fluorochrome-conjugated antibodies: CD38 (HIT-2, BD), IgD (IA6-2, BD), IgM (MHM-88, BioLegend), CD10 (HI10a, BD), CD19 (SJ25C1, BD), CD21 (B-ly4, BD), CD27 (0323, eBiosience), CD138 (B-B4, AbD SeroTec), IgG (SouthernBioTech #2043-09), IgA (G20-359, BD), CD3 (SK7, BD), CD28 (CD28.2, BD), FOXP3 (PCH101, eBioscience), CD8 (SK1, BD), CD4 (RPA-T4, eBioscience), γδ-TCR (B1.1, eBioscience), αβ-TCR (IP26, eBioscience), CD45RO (UCHL1, BD), CD45RA (HI100, BD), CD57 (NK-1, BD), CD31 (WM59, eBioscience), CD62L (DREG-56, BD), CD152/CTLA4 (BNI3, BD). Samples were acquired on a FACS-Canto II flow cytometer (BD) or on a Gallios flow cytometer (Beckman Coulter, Miami, FL) and analyzed using FlowJo version 7.6.5 analysis software (Treestar, Ashland, OR).
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5

Isolation and Sorting of CD8+ T Cell Subsets

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PBMCs were isolated from fresh whole blood using Ficoll-Paque Plus (GE) density gradient centrifugation. For cell sorting, we used fluorochrome-labeled antibodies specific for CD3 (UCHT1), CD27 (M-T271) (Biolegend), CD4 (RPA-T4), CD19 (HIB19), IgD (IA6–2), CD127 (HIL-7R-M21) (BD Biosciences), and CD8 (SCF121Thy2D3) (Beckman-Coulter). CD8+IL7R+ (CD8+CD127+) and CD8+IL7R (CD8+CD127) T cells were sorted from the CD19CD3+CD4 fraction. Cell sorting was performed using FACSAria Fusion (BD).
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6

Phenotyping SARS-CoV-2-specific B Cells

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Freshly isolated or thawed PBMCs were stained first for viability with LIVE/DEAD Fixable Yellow (Thermo Fisher Scientific) and then for markers with the following mAbs: IgA (IS11-8E10; Miltenyi Biotec), IgD (IA6-2; BD Biosciences), IgG (G18-145; BD Biosciences), IgM (MHM-88; BioLegend), CD3 (SK7, BD Biosciences), CD4 (RPA-T4, BD Biosciences), CD8 (SK1; BD Biosciences), CD14 (61D3; eBioscience), CD16 (CB16; eBioscience), CD19 (SJ25C1; BD Biosciences), CD20 (2H7; BD Biosciences), CD27 (O323; BioLegend or MT271; BD Biosciences), CD38 (HB7; BD Biosciences), and CD71 (CY1G4; BioLegend). Ag-specific B cells were detected by staining with RBD-conjugated to Alexa Fluor 488 (Alexa Fluor 488 Protein Labeling Kit; Thermo Fisher Scientific). RBD was conjugated as previously described.4 (link) After staining, PBMCs were washed and then fixed for 15 min using 2% paraformaldehyde (PFA; Thermo Fisher Scientific). Data were acquired on a BD FACSymphony A5 and analyzed using FlowJo 10.8.0 (BD Biosciences).
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