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17 protocols using anti cd19 apc cy7

1

Sorting and Phenotyping of B Cell Subsets

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Peripheral B cells were purified from the blood of patients and control donors by positive selection using CD20 magnetic beads (Miltenyi Biotec). For sorting, enriched B cells were stained with FITC-anti-IgM, PE-anti-IgG, PE-Cy7-anti-CD10, APC-anti-CD21, Pacific Blue-anti-CD19, and PercP-Cy5.5-anti-CD27 (all from BioLegend) (gating strategy is shown in fig. S21). Single- or batch-sorted CD19+CD21loCD10+IgMhiCD27 new emigrant and CD19+CD21+CD10IgM+CD27 mature naïve B cells from patients, heterozygous relatives, and HDs were sorted on a FACSAria flow cytometer (Becton Dickinson, Mountain View, CA) into 96-well polymerase chain reaction (PCR) plates or 5-ml round-bottom polystyrene test tubes, respectively. For phenotyping, enriched B cells were stained with FITC-anti-IgM, PE-anti-CD69, PE-Cy7-anti-CD10, APC-anti-CD86, PercP-Cy5.5-anti-CD27, APC-Cy7-anti-CD19 (all from BioLegend), and V450-anti-CD21 (BD Bioscience) (gating strategy is shown in fig. S22).
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2

Multiparametric Analysis of PBMCs

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Total PBMCs cells were stained with Pacific Blue anti-CD3 (BD 558117, clone UCHT1), PerCP-anti-CD4 (BD 566924, clone SK3), APC-Cy7-anti-CD8 (BD 557834, clone SK1), FITC-anti-CD45RA (BD 555488, clone HI100), and PE-anti-CD45RO (BD 555493, clone UCHL1) antibodies or APC-Cy7-anti-CD19 (BioLegend 302218, clone HIB19), Pacific Blue-anti-CD27 (BioLegend 356414, clone M-T271), FITC-anti-IgD (Life Technology H15501), and PerCP-anti-CD3 (BioLegend 300326, clone HIT3a). After 30 minutes of incubation, cells were washed, fixed, and permeabilized using the Foxp3/transcription factor staining buffer set (Thermo Fisher Scientific) according to the manufacturer’s instruction. Cells were then intracellularly stained with an Alexa Fluor 647-anti-AIOLOS antibody (BD 565215, clone S50-895) for an hour. Cells were acquired and analyzed by flow cytometry (Becton Dickinson FACSCanto II) and FlowJo software (FlowJo 10.8.2, TreeStar), respectively.
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3

Immunophenotyping and Proliferation of B-1 Cells

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For ex vivo analysis of B‐1 cells, 1 × 106 single cells from PL, BM, or spleen were incubated with anti‐mouse CD16/32 (Biolegend) for 15 min on ice for blocking of unspecific Fc‐binding sites. Subsequently, cells were stained with anti‐CD19 FITC, anti‐CD43 PE‐Cy7, anti‐CD5 APC, anti‐IgM APC‐Cy7, and anti‐CD138 PE antibodies (Biolegend and BD Bioscience) for 15 min on ice. To assess cell death, cells were incubated with 7‐aminoactinomycin D (BD Bioscience) before analysis for at least 15 min, but no longer than 60 min.
To analyze proliferation and surface immune globulins after in vitro stimulation, CFSE‐stained cells were incubated with anti‐CD19 V450, anti‐CD43 PE‐Cy7, anti‐CD5 APC, anti‐IgM APC‐Cy7, anti‐IgD‐PerCP, and anti‐IgG1 PE (LPS/IL‐4) or with anti‐CD19 APC‐Cy7, anti‐CD43 PE, anti‐CD5 APC, anti‐IgA BV421, anti IgG2ab BB700, and anti‐IgG3 PE‐Cy7 (LPS only) (Biolegend and BD Bioscience).
All measurements were performed at the BD FACS Canto II and biaxial gating was done with FlowJO Version 10.
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4

NK Cell-Mediated CD4 T Cell Cytotoxicity

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Uninfected CD4 T cells were isolated as above and treated or not with HDACi at the indicated doses. Meanwhile NK cells were isolated as above. NK and CD4 T cells were cultured at a 1:1, 1:0.2, or 1:0.01 ratio for 5 hours at 37°C in the presence of an anti-CD107a PE-Cy7 antibody (Biolegend). Experiments using K562 cells were performed at a 1:1 ratio for 5 hours as with CD4 T cells. For both CD4 T and K562 experiments, cells were then washed and stained with a panel of: LIVE/DEAD fixable near-IR dead cell stain kit (Life Technologies), anti-CD3 eflour450 (eBioscience), anti-CD56 APC (Miltenyi), anti-CD16 FITC (Biolegend), anti-CD14 APC-Cy7 (Biolegend), anti-CD19 APC Cy7 (Biolegend). NK cells were gated on APC Cy7 negative cells (live, CD14-, CD19-), CD3 negative, CD56 positive cells.
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5

NK Cell Phenotyping after HDAC Inhibition

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PBMC were cultured for 24h in the absence or presence of 100nM panobinostat, 20nM panobinostat, or 10nM romidepsin. After culture, wells were stained with a panel of: LIVE/DEAD fixable near-IR dead cell stain kit (Life Technologies), anti-CD3 eflour450 (eBioscience), anti-CD16 APC (Cambridge Bioscience), anti-CD56 FITC (Cambridge Bioscience), anti-CD14 APC-Cy7 (Biolegend), anti-CD19 APC Cy7 (Biolegend), NKG2D PECy7 (Cambridge Bioscience), and CD335 (NKp46) PE (Miltenyi Biotec). NK cells were gated on APC Cy7 negative cells (live, CD14-, CD19), CD3 negative, CD56 positive cells.
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6

Flow Cytometry Staining of MR1 Tetramers

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SKW-3.β2mnull.CD8αα or SKW-3.β2m null.CD8αβ (105 per sample) were stained with MR1 or MHC-I tetramers in PBS + 2% FBS for 20 min at 4°C in the dark. Cells were washed with PBS + 2% FBS and resuspended in a surface antibody stain consisting of anti-CD3-BV421 (#562426, UCHT1; BD Horizon), anti-CD8α-BUV805 (#564912, SK1; BD Horizon), anti-CD8β-APC (#641058, 2ST8.5H7; BD FastImmune), and LIVE/DEAD fixable Near-IR dead cell stain (#L10119; Thermo Fisher Scientific) for a further 20 min at 4°C in the dark. Cells were washed twice with PBS + 2% FBS and data were acquired using a BD LSR Fortessa (BD Biosciences). PBMCs were stained with MR1 tetramers as described in (Souter et al., 2019 (link)). In brief, PBMCs (107 per sample) were stained with MR1 tetramer in PBS + 2% FBS for 30 min at room temperature in the dark, washed with PBS + 2% FBS, and stained with surface antibodies anti-CD3-BV421, anti-CD19-APC-Cy7 (#302218, HIB19; Biolegend), anti-CD14-APC-Cy7 (#557831, MφP9; BD Pharmingen), anti-CD8α-BUV805, anti-CD8β-APC, anti-CD161-PE-Vio770 (#130-113-597, REA631; Miltenyi Biotec), anti-CD4-AF700 (#557922, RPA-T4; BD Pharmingen), and LIVE/DEAD fixable Near-IR dead cell stain for 20 min at 4°C. Cells were washed twice and resuspended in PBS + 2% paraformaldehyde (PFA) before data acquisition on a BD LSR Fortessa.
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7

Multiparametric Flow Cytometry Panel

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The following antibodies were used for flow cytometric stainings anti-TACI PE (clone 1A1), anti-CD19 APC-Cy7, anti-CD27 PerCP-Cy5.5 or APC, anti-CD10 PE-Cy7, anti-IgM FITC, anti-CD21 APC, anti-CD69 PE-Cy7, anti-CD86 PE, anti-CD4 APC-Cy7, anti-CD25 PECy7, anti-CD127 PerCP-Cy5.5, anti-CD45RO Pacific Blue, anti-CXCR5 PerCP-Cy5.5, anti-PD-1 PE-Cy7, anti-CD25 PE, anti-CD25 PE-Cy7 (all from BioLegend, San Diego, Calif), anti-CD3 eFluor 605NC, anti-CD21 BD Horizon V450 (Becton Dickinson) and goat polyclonal anti-TACI biotin (R&D Systems). Intracellular staining with anti-Foxp3 Alexa Fluor 488 and anti-BCL6 PE (eBioscience, San Diego, Calif) was performed using the Foxp3/Transcription Factor Staining Buffer Set (eBioscience), in accordance with the manufacturer's instructions.
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8

Phenotyping Vaccinated PBMC Subsets

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Phenotype of vaccinated individuals’ PBMCs was determined by flow cytometry with the following antibodies: anti-CD20-BV510 (2H7, 1:80), anti-IgM-BV605 (MHM-88, 1:200), anti-CD71-FITC (CY1G4, 1:1000), anti-CD95-PE-Dazzle594 (DX2, 1:50), anti-CD24-FITC (ML5, 1:100), anti-CD38-PE-Cy7 (HB-7, 1:300), anti-BAFF-R-AF647 (11C1, 1:100), anti-CD19-APC-Cy7 (HIB19, 1:150) (BioLegend); anti-IgG-BV650 (G18-145, 1:600), anti-CD27-BV786 (L128, 1:100), anti-CD69-BV480 (FN50, 1:200) (BD Biosciences); anti-IgA-PerCP (polyclonal, 1:200) (Jackson ImmunoResearch); anti-CD3-SB-436 (OKT3, 1:200), anti-CD33-Super Bright 436 (WM-53, 1:50), anti-IgD-PerCP-eFluor 710 (IA6-2, 1:200) (Invitrogen). Dead cell exclusion was performed by Zombie NIR Fixable Viability Kit (Biolegend, 1:800). Multiparametric flow cytometry data was collected on Cytek Aurora with SpectroFlo Software version 2.2.0.3.
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9

Antibody Panel for ULBP4 Detection

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Anti-ULBP4 mAb (clone 709116) was purchased from R&D (Minneapolis, MN, USA). The ULBP4-specific mAb DUMO1 was previously described [32 (link)]. Anti-CD3-PerCP-Cy5.5 and fixable viability dye(FVD)-eFluor506 were from eBioscience (SanDiego, CA, USA), anti-CD19-APC-Cy7, anti-CD14-FITC, anti-NKp46-PE-Cy7, streptavidin-BV421 (SA-BV421) and goat-anti-mouse-IgG-PE (GaM-PE) were from Biolegend (SanDiego, CA, USA).
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10

Comprehensive Immunophenotyping of Immune Cells

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Anti-CD19 APC-Cy7, anti-CD38 PerCp-Cy5.5, anti-CD4 PE-Cy7, anti-CD25 PerCP-Cy5.5, anti-CD86 APC, anti-CD80 BV421, anti-CD45RA BV605, anti-ICOS PE, anti-CD21 PE-Cy7, anti-CD80 BV421, anti-CD27 PerCp-Cy5.5, anti-PD-1 APC, anti-CD45RA APC-Cy7, anti-HLA-DR BV605, anti-CD11c AF700, anti-CD86 BV711, anti-CD95 BV650, anti-IgD BV786, anti-FCRL5 APC, anti-CXCR3 BV421, anti-CCR6 BV605, anti-CD19 BV650, anti-CD19 BV605, anti-PD-L1 BV421, anti-PD-L2 PE, anti-ICOS-L PE, anti-OX40L PE, anti-IL-10 PE, anti-IL-10 APC, anti-TNF-α APC-Cy7 (all obtained from BioLegend); anti-IgD FITC and anti-IgD PE (both from Southern Biotech); anti-CD27 PE (Dako); and anti-CD21 PE-Cy7, anti-CD69 FITC, anti-HLA-DR FITC, anti-CD27 BV605, anti-CD40 FITC, anti-CD40L PE, anti-ICAM-1 PE, anti-CXCR5 BUV395 and anti-CD27 BUV395 (all from BD Biosciences).
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