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10 protocols using nkg2a pe

1

Comprehensive NK Cell Phenotyping

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Flow cytometry was performed on cryopreserved cells. As per the gating strategy in figure 1A, NK cells were identified using a combination of Fixable blue dead cell stain (Life technologies), CD3-Pacific Blue, CD56-PE-Cy7 and CD16- APC-Cy7 (BD Biosciences). NK cell receptor expression was assessed using combinations of CD158a-PerCP-Cy5.5 (eBioscience), CD158b-FITC, KIR3DL1-Alexafluor700 (both Biolegend), KIR2DL3-PE, KIR2DL1-APC (both R&D Systems), NKG2A-PE (Beckman Coulter), NKG2D-APC, CD94-FITC, 2B4-FITC, NKp46-PE, NKp30-APC (all BD Biosciences), TRAIL-PE (Biolegend), CD161-FITC (Miltenyi) and CD160-Alexafluor647 (Biolegend). For intracellular staining, cells were fixed and permeabilized (PermA/B solution, Caltag) according to the manufacturers' instructions, prior to incubation with Perforin-PerCP-Cy5.5 (eBioscience). At least 1500 NK cells were acquired for all samples on either a five laser BD LSRFortessa or a four laser BD LSRII system, equipped with FACSDiva Version 8.8.3 (BD biosciences). Rainbow beads ensured a consistent, comparable level of fluorescence across all samples on different days of acquisition. Gates were set using fluorescence minus one or unstimulated samples where appropriate. The data were analysed using FlowJo version 9.5.3 (Treestar, OR, USA).
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2

Multiparametric Flow Cytometry Analysis

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Antibodies to the following antigens were included in this study and except where noted, all were obtained from BD Biosciences: α4β7-APC (clone A4B7, NHP reagent resource), active-caspase-3-Alexa647 (clone C92-605), CCR7-Alexa700 (clone 150503, R&D Systems), CD3-APC-Cy7 (clone SP34.2), CD4-FITC (clone L-200), CD16-Alexa-700 (clone 3G8), CD45-FITC (clone D058-1283), CD45-PerCp-Cy5.5 (clone Tu116), CD56-PE-Cy7 (clone NCAM16.2), CD62L-FITC (clone SK11), CXCR3-PE-Cy5 (clone 1C6), HLA-DR-PE-Texas Red (clone Immu-357, Beckman-Coulter), NKG2A-PE (clone Z199, Beckman-Coulter), NKG2A-Pacific Blue (clone Z199, in-house custom conjugate, Beckman-Coulter), NKp44-PerCp-Cy5.5 (clone Z231, Beckman-Coulter), Ki67-FITC (clone B56), Perforin-Pacific Blue (in-house custom conjugate, clone Pf-344, Mabtech). Flow cytometry acquisitions were performed on an LSR II (BD Biosciences, La Jolla, CA) and FlowJo software (version 9.6.4, Tree Star Inc., Ashland, OR) was used for all analyses. Pestle (Version 1.6.2) and SPICE (Version 5.1) were used for multi-parametric analyses.
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3

Comprehensive NK-Cell Receptor Profiling

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Cryopreserved peripheral blood mononuclear cells (PBMC) were stained with combinations of antibodies that comprehensively interrogate the breadth of NK-cell receptors including the killer immunoglobulin receptors (KIRs), the c-type lectin receptors (NKG2), and the natural cytotoxicity receptors (NCRs). These included CD158a-PerCP-Cy5.5 (eBioscience), KIR3DL1-Alexafluor700 (Biolegend), NKG2A-PE (Beckman Coulter), NKG2D-APC, CD94-FITC, 2B4-FITC, NKp46-PE, NKp30-APC, CD158b-FITC (all BD Biosciences), TRAIL-PE (Biolegend), CD161-FITC (Miltenyi) and CD160-Alexafluor647 (Biolegend). Dead cells were excluded using the Fixable Blue Dead Cell Stain (Life Technologies) prior to surface staining and fixation. For perforin staining, samples were then permeabilized (Perm A/B, Caltag) and stained with anti-Perforin-PerCP-Cy5.5 (eBioscience). NK cells were identified as CD3 negative lymphocytes expressing CD56 and/or CD16. At least 1500 NK cells were acquired per sample. Fluorescence minus one was used to set gates. The data were analyzed with Flowjo v9.5.4 (Treestar).
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4

Flow Cytometry Immunophenotyping Protocol

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The following antibodies were used for flow cytometry: CD3 Alexa 700 (SP34-2 BD Biosciences), CD4 AmCyan (L200 BD Biosciences), CD8 PerCP-Cy5.5 (SKI eBiosciences), CD8 AmCyan (SKI BD Biosciences), CD28 PE-Texas Red (CD28.2 Beckman Coulter, BD Biosciences), CD95 PE (DX2 BD Biosciences, eBiosciences), CCR5 Allophycocyanin (3A9 BD Biosciences), Ki-67 FITC (B56 BD Biosciences), CD56 PerCP-Cy5.5 (MEM-188 Invitrogen), CD16 Pacific Blue (3G8 BD Biosciences, Biolegend), CD20 Allophycocyanin-Cy7 (L27 BD Biosciences), HLA-DR PE-Texas Red (TU36 Invitrogen, Immu357 Beckman Coulter), NKG2A PE (Z199 Beckman Coulter), CD14 FITC (M5E2 BD Biosciences, R&D Systems), STAT5 PE (47/Stat5 (pY6) BD Biosciences), BrdU FITC (B44 BD Biosciences), BrdU Allophycocyanin (B44 BD Biosciences). Anti-CCR7 (150503) was purchased as purified immunoglobulin from R&D Systems, conjugated to biotin using a Pierce Chemical Co. biotinylation kit, and visualized with streptavidin–Pacific Blue (Invitrogen). Rhesus recombinant anti-IL-15 and rhesus recombinant control IgG1 mAb were provided through the National Institutes of Health’s Nonhuman Primate Reagent Resource Program. Simian recombinant IL-7 was provided by Cytheris SA (Issy-Les-Moulineaux, France). Rhesus recombinant IL-15 was provided by Francois Villinger (Emory University) through the Resource for Nonhuman Primate Immune Reagents.
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5

Flow Cytometric Analysis of NK Cell Receptors

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The following antibodies were used for flow cytometry (all anti-human): CD16-PE (BD Biosciences, 560995, clone 3G8), CD16-APC (BD Biosciences, 561248, clone 3G8) NKG2D-PE (BD Biosciences, 557940, clone 1D11), NKp44-PE (BD Biosciences, 558563, clone p44-8), NKp46-PE (BD Biosciences, 557991, clone 9E2), TRAIL-PE (BD Biosciences, 565499, clone YM366), FAS ligand-PE (BD Biosciences, 56426, clone NOK-1), NKG2A-PE (Beckman Coulter, IM3291U, clone Z199), CD158a,h (KIR2DL1, KIR2DS1)-PE (Beckman Coulter, A09778, clone EB6B), CD158b1/b2,j (KIR2DL2, KIR2DL3, KIR2DS2)-PE (Beckman Coulter, IM2278U, clone GL183), CD158e1(KIR3DL1)-BV421 (BioLegend, 312713, clone DX9), CD158a(KIR2DL1)-APC (Miltenyi, 130-120-584, clone REA284), CD158b1/b2,j (KIR2DL2, KIR2DL3, KIR2DS2)-PE-Cy5.5 (Beckman Coulter, A66900, clone GL183), CD158a,h(KIR2DL, KIR2DS1)-PE-Cy7 (Beckman Coulter, A66899, clone EB6B), CD158b2(KIR2DL3)-PE, (R&D systems, FAB2014P, clone 180701), CD155-PE (BioLegend, 337609, Clone SKII.4), HLA E-PE (BioLegend, 342603, Clone 3D12) MICA/MICB-PE (BD Biosciences, 558352, Clone 6D4), CD112-PE (BD Biosciences, 551057, Clone R2.525), ULBP2/5/6-PE (R&D Systems, FAB1298P, Clone 16590).
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6

Phenotyping of NK Cell Subsets

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The monoclonal antibodies CD3‐PerCP, CD56‐allophycocyanin(APC), CD158a‐FITC, CD158b‐PE, CD158e‐FITC, CD94‐FITC, CD62L‐FITC, CD54‐PE, CD11a‐FITC, CX3CR1‐FITC, CXCR4‐PE, CCR7‐PE, NKP30‐FITC, NKP46‐PE, IL13‐PE, IL10‐PE, TGF‐β‐PE and IFN‐γ‐FITC (BD Bioscience, Mountain View, CA, USA), and NKG2A‐PE (BeckmanCoulter, USA) and appropriate isotypes were used in individual 4‐colour flow cytometry assays to analyse the immunophenotype as well as the cytokine secretion of NK cells. Intracellular staining was performed using the Pharmingen Intracellular Staining Kit (BD Pharmingen, San Diego, CA, USA). The cells were incubated for 5 hours with phorbol myristate acetate (PMA) (40 ng/mL) plus ionomycin (2.5 μg/mL, all reagents from Sigma Chemical) to stimulate maximal IFN‐γ, IL‐13, TGF‐β and IL‐10 production; GolgiStop (0.7 μL/mL) was added to the sample during the last 4 hours to trap the protein in the cytoplasm. NK1, NK2, NK3 and NKr cells were identified as CD3CD56+IFN‐γ+, CD3CD56+IL‐13+,CD3CD56+ TGF‐β+ and CD3CD56+IL‐10+, respectively. The dose of NK1, NK2, NK3 and NKr cells was classified as the absolute number of NK1, NK2, NK3 and NKr cells infused in GBM and GPB (cells/kg). Data were analysed using a FACSCaliber 4‐colour flow cytometer (BD Biosciences) and FlowJo 7.6.1 software (Tree Star Inc, CA, USA).
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7

Intracellular Analysis of NK Cell Activation

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KB tumor cells were treated with C-IgG– or F-IgG–FITC for 30 min at 37°C and collected at the designated time points. Cells were washed with flow buffer (5% FBS in PBS), fixed in 1% formalin in PBS, mounted on 25 × 75 × 1 mm slides (Erie Scientific, Portsmouth, NH) and stained with DAPI for nuclear identification (Vector Labs, Burlingame, CA) prior to analysis by immunofluorescence (IF) microscopy. Intracellular analysis of NK cell ERK phosphorylation was also assessed following coculture with KB tumor cells. NK cell activation was assessed 48 hours post coculture via FACS analysis with CD56‐phycoerythrin (PE), CD158-allophycocyanin (APC), CD57‐FITC, NKG2A-PE (Beckman Coulter, Brea, CA), CD56‐APC, CD3‐V450, CD16‐FITC, NKG2D-APC, CD69–phycoerythrin-cyanin 7 (Pe-Cy7) and KIR/NKAT2‐FITC, CD94‐APC, NKp46/CD335-APC antibodies (BD Biosciences, San Jose, CA). In murine studies, IF microscopy of tumor sections was performed (16 (link)). Sections were analyzed on an Olympus Fluoview 1000 laser scanning confocal microscope. In murine studies with C‐IgG– and F‐IgG–FITC, tissues were harvested in the dark at indicated times. Tumors were dissociated (17 (link)) and stained with FR‐α–APC (R&D Systems, Minneapolis, MN). FR+/FITC+ populations were assessed using a Becton Dickinson FACS Calibur flow cytometer (Becton‐Dickinson, San Jose, CA) (16 (link)).
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8

Profiling Immune Cell Subsets Post-Vaccination

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On days 0, 1, and 14 after the first immunization, the cellular composition of the PBMCs was analyzed using flow cytometry. Freshly isolated PBMCs were stained with Live/Dead Fixable Blue Dye (Life Technologies, cat# L-23105, 1:40 dilution) and FcR blocking reagent (Miltenyi Biotec, cat# 130-059-901, 1:20 dilution) followed by a panel of antibodies: CD40 FITC (5C3, Biolegend, cat# 334306, 1:20 dilution), NKG2A PE (Z199, Beckman Coulter, cat# IM3291U, 1:40 dilution), CD80 BV421 (L307.4, BD, cat# 564160, 1:40 dilution), CCR7 PE-Dazzle594 (G043H7, Biolegend, cat# 353236, 1:50 dilution), CD123 Per-CP-Cy5.5 (7G3, BD, cat# 558714, 1:80 dilution), CD3 APC-Cy7 (SP34-2, BD, cat# 557757, 1:80 dilution), CD66 APC (TET2, Miltenyi Biotec, cat# 130-118-539, 1:80 dilution), CD70 BV786 (Ki-24, BD, cat# 565338, 1:80 dilution), HLA-DR BV650 (L243, Biolegend, cat# 307650, 1:80 dilution), CD11c PE-Cy7 (3.9, Biolegend, cat# 301608, 1:160 dilution), CD16 AF700 (38 G, BD, cat# 560713, 1:160 dilution), CD20 BV605 (2H7, Biolegend, cat# 302334, 1:160 dilution) and CD14 BV510 (M5E2, Biolegend, cat# 301842, 1:160 dilution). After washing with PBS, samples were fixed using 1% paraformaldehyde (PFA) and acquired on a BD LSRFortessa cell analyzer. The data were analyzed using FlowJo software v.10.7.1 (FlowJo).
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9

Comprehensive NK-Cell Receptor Profiling

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Cryopreserved peripheral blood mononuclear cells (PBMC) were stained with combinations of antibodies that comprehensively interrogate the breadth of NK-cell receptors including the killer immunoglobulin receptors (KIRs), the c-type lectin receptors (NKG2), and the natural cytotoxicity receptors (NCRs). These included CD158a-PerCP-Cy5.5 (eBioscience), KIR3DL1-Alexafluor700 (Biolegend), NKG2A-PE (Beckman Coulter), NKG2D-APC, CD94-FITC, 2B4-FITC, NKp46-PE, NKp30-APC, CD158b-FITC (all BD Biosciences), TRAIL-PE (Biolegend), CD161-FITC (Miltenyi) and CD160-Alexafluor647 (Biolegend). Dead cells were excluded using the Fixable Blue Dead Cell Stain (Life Technologies) prior to surface staining and fixation. For perforin staining, samples were then permeabilized (Perm A/B, Caltag) and stained with anti-Perforin-PerCP-Cy5.5 (eBioscience). NK cells were identified as CD3 negative lymphocytes expressing CD56 and/or CD16. At least 1500 NK cells were acquired per sample. Fluorescence minus one was used to set gates. The data were analyzed with Flowjo v9.5.4 (Treestar).
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10

Quantifying T cell populations in rhesus macaques

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Whole blood was stained at specific pre- and during treatment time points to monitor the impact of treatment on major immune cell populations. The two-step TruCount (BD Bioscience) technique was used to enumerate the absolute number of CD4+ and CD8+ T cells in blood18 (link),60 (link). Blood was stained with fluorescently-labeled antibodies (antibodies from BD Bioscience, San Jose, CA, USA, except where noted): CD4 (APC, cat# 551980, 2.5 μl), CD8 (PE-CF594, cat#: 562282, 3 μl), CD3 (V450, cat#: 560351, 2 μl), CD45 (PerCP, cat#: 558411, 3 μl), NKG2A (PE, Beckman Coulter Life Sciences, Indianapolis, IN, USA, cat#: IM3291U, 5 μl). In addition, Ki-67 (PE, cat#: 556027, 20 μl) was stained post fixing and permeabilizing cells after the surface staining. Flow cytometry acquisitions were performed on an LSR II flow cytometer (BD Biosciences, with FACSDiva v8.01, and FlowJo v10.4, v10.7.1). All antibodies were used following the manufacturers’ recommendations, and validation for use of these antibodies in rhesus macaques was ascertained by the NIH (as indicated in www.nhpreagents.org/ReactivityDatabase).
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