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11 protocols using cd3 apc h7 clone sk7

1

ICOS and Tbet Expression in PBMCs

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PBMCs were counted and 1 × 106 cells were resuspended in flow buffer (PBS+2% FBS, 1 mmol/L EDTA, and 0.1% sodium azide) containing CD3-APC-H7 (clone SK7, BD Biosciences) and CD4-PerCP-Cy5.5 antibodies (clone L200, BioLegend) for 30 minutes at 4⁰C. After washing with flow buffer, cells were permeabilized and fixed using the FOXP3 Fixation/Permeabilization Concentrate and Diluent Kit (eBioscience) according to the manufacturer's instructions. Permeabilized cells were stained with biotinylated anti-human ICOS antibody (clone: M13, Jounce Therapeutics, a noncompetitive binder to ICOS compared with vopratelimab) for 30 minutes at 4°C. After washing, cells were incubated with streptavidin-PE (BioLegend) for 30 minutes at 4°C, washed and then resuspended in flow buffer. In some experiments, Tbet-BV421 (clone 4B10, BioLegend) was added at the intracellular staining step.
Flow cytometry was performed on the same day using the FACSCanto II or LSR Fortessa (BD).
After January 2019, all clinical samples were analyzed at FlowMetric. The same method, flow panel, and analysis were followed at both Jounce and FlowMetric.
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2

Isolation and Characterization of PBMC Subsets

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PBMCs were washed 3× with RPMI1640 culture medium (Gibco, Thermo Fisher Scientific Inc., Waltham, MA, USA) and resuspended in complete culture medium (CM: RPMI1640 supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 50 µM 2-mercaptoethanol), at a concentration of 106 cells/mL. PBMCs were cultured in triplicate in a 37 °C humidified chamber with 5% CO2 for 12 h, in the presence or absence of mitogens (PI: 5 ng/mL phorbol myristate acetate and 1 μM ionomycin) (Sigma-Aldrich, Merck KGaA) or recombinant human leptin (R&D Systems) at a concentration of 200 or 500 or 800 ng/mL. At the end of culture, CD3+ T cells and CD14+ monocytes were isolated by cell sorting using a BD FACS Aria II flow cytometer (BD Biosciences, San Jose, CA, USA). The sorting strategy is shown in Figure 8. The enriched cell populations were used when purity was >95% for T cells and >90% for monocytes. The antibodies used for cell sorting and phenotyping were mouse monoclonal anti-human antibodies CD3-APC-H7 (clone SK7) and CD14-FITC (clone M5E2) (BD Biosciences). Fluorescence-minus-one (FMO) controls were used to identify any background spread of fluorochromes and to establish gating limits. Data were analyzed using BD FACS DIVA v.9 software (BD Biosciences).
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3

Flow Cytometric Analysis of MMP-9 and TIMP-1

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Cells were stained with the following monoclonal antibodies; CD3- APC/H7 clone SK7 (BD Biosciences, San José, CA, US) and CD14-PeCy7 clone M5E2 (Nordic Biosite, Täby, Sweden). Whole blood and antibodies were incubated for 15 minutes at RT, thereafter erythrocytes were lysed with FACS Lysing Solution (BD Biosciences) for 15 minutes at room temperature (RT). The cells were permeabilized for 30 min at RT with Permeabilizing Solution 2 (BD Biosciences) and washed with Permeabilization buffer (Ebioscience, San Diego, CA, USA). Unspecific binding was blocked with 10% FCS and thereafter, cells were stained with antibodies against MMP-9 and TIMP-1, conjugated with FITC and PE respectively, (RnD Systems) for 30 min in 4°C. After washing in Permeabilization buffer followed by resuspension in PBS with 0.5% FCS, cells were analyzed using Beckman Coulter Gallios (Beckman Coulter, Miami Lakes, Florida, US). The obtained data was analyzed and visualized using the Kaluza 1.2 software (Beckman Coulter). When this analysis was performed, antibodies against TIMP-2 were not commercially available.
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4

Cytotoxic Immune Cell Profiling

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Single cell suspensions were stained with CD4-FITC (clone OKT-4), TCR γ/δ-FITC (clone B1), TCR Vα7.2-APC (clone 3C10), CD107a-Brilliant Violet 650 (clone H4A3), Perforin-PE (clone dG9) (All from Biolegend Inc., San Diego, USA), CD3-Brilliant Violet 711 (clone UCHT1), CD3-APC-H7 (clone SK7), CD8-Brilliant Violet 711 and -Alexa Fluor® 700 (clone RPA-T8), CD45-PerCP (clone 2D1), GrB-PE and -Alexa Fluor® 700 (clone GB11) (BD Biosciences™), and CD161-eFluor450 (clone HP-3G10) (eBioscience). Lymphocytes were identified by their forward and side scatter characteristics, and LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (molecular probes® by Life Technologies) was used to gate out dead cells. FIX&PERM® (AN DER GRUB Bio Research GmbH) intracellular staining kit was used for detection of cytokines. Isotype controls were used to determine cut-off levels for positive perforin staining, and cut-off levels for GrB and CD107a were guided by expression in circulating conventional CD8+ T cells, which have distinct GrB+ and GrB populations and are CD107a. Data was acquired using a Becton Dickinson LSR II flow cytometer and analyzed by FlowJo software.
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5

Phenotyping Immune Checkpoint Profiles in PBMCs

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Peripheral blood mononuclear cells (PBMC) were isolated from peripheral blood and leukapheresis by Ficoll-Hypaque density gradient centrifugation and cryopreserved in liquid nitrogen. Cryopreserved PBMCs were thawed, washed, and stained with the following fluorophore-conjugated antibodies: CD3-APC-H7 (clone SK7, BD#560176), CD4-APC (clone SK3, BD#340443), CD38-BV421 (clone HIT2, BD#562444), TIGIT-PE (clone MBSA43, ebioscience#12–9500), PD-1- PE-Cy7 (clone eBioJ105, ebioscience#25–2799), LAG-3-PerCP-eF710 (clone 3DS223H, ebioscience#46–2239), TIM-3-FITC (clone F38-2E2, ebioscience#11–3109). Data were acquired on a BD FACSCanto II flow cytometer using the FACSDiva software (Becton Dickinson) and analyzed using Flow Jo version 10.1r5. Flow cytometry was repeated on specimens from select patients to ensure reproducibility.
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6

Phenotyping Tumor-Infiltrating Lymphocytes

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Tumor-infiltrating lymphocytes and NILs were washed and suspended in 100-µL staining solution (PBS with 2% serum and 0.1% sodium azide). Cells were then incubated with FcR blocker (Miltenyi Biotec, Bergisch Gladbach, Germany) for blocking Fc receptor and 7AAD dye was used to discriminate between live and dead cells. For identification of immune cells, TILs and NILs were stained with cell surface antibodies CD45-FITC (clone HI30, eBioscience, San Diego, CA, USA), CD3-APC.H7 (clone SK7, BD Biosciences, Oxford, UK), CD4-Alexa Fluor 700 (clone RPA-T4, BioLegend, San Diego, CA, USA), CD25-PE/Cy7 (clone M-A251, BioLegend), PD-1-PE/Dazzle™ 594 (clone EH12.2H7, BioLegend), and CD39-PerCP/Cy5.5 (clone A1, BioLegend) for 30 min at 4°C. After staining, cells were washed and cell pellet was resuspended in flow cytometry staining buffer (eBioscience).
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7

Phenotypic Characterization of Activated T Cells

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Fifteen thousand DCs were prepared as described in 2.7 and cocultured with 150,000 autologous CD3+ T cells at a concentration of 1 × 106 T cells/ml. After 5 days of coculture, T cells were harvested, washed with PBS and stained for 15 min at the dark using the following anti-human mAbs: CD3 APC-H7 (clone SK7, BD Biosciences), CD4 Pe-Cy7 (clone SK-3, Thermofisher), CD8 PE (clone SK1, BD Biosciences), CD279/PD-1 APC (clone MIH4, Thermofisher), CD197/CCR7 Alexa Fluor 647 (clone G043H7; Biolegend), and CD45RA V500 (clone HI100; Biolegend). Unstimulated CD3+ T cells were used as negative control, and unstained CD3+ T cells were used as negative fluorescence control. At least 10,000 events of each sample were collected and analyzed at FACS Canto II Flow Cytometer (BD Biosciences).
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8

Quantifying Activated NK Cells in Myeloma

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To assess the activation of CD3CD16+CD56+ NK cells, cells were stained with CD16 PE (clone 3G8 or B73.1), CD56 PE (clone MY31), and CD3 APC H7 (clone SK7) to identify NK cells, and CD54 APC (clone HA58) and CD25 PEcy7 (clone MA-251) (all from BD Biosciences, San Diego, CA) to assess activation status. Dead cells were gated out using propidium iodide. Lenti-GFP-OPM2 cells were used in the assay to facilitate the gating of myeloma cells from the PBL. To quantify the number of myeloma cells, 30 μL of FITC-QuantiBRITE® beads (Polysciences, Inc.) containing approximately 30,000 beads was added to each tube at the time of staining. Data were acquired on FACSCanto™ (Becton–Dickinson), and acquisition was stopped when 5,000 bead events were acquired. Data were analyzed using FACS DIVA software.
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9

Mouse Anti-Human Flow Cytometry Antibodies

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The following mouse anti-human flow cytometry antibodies were used in this report:

CD3 APC-H7 (clone SK7) cat no. 641406 (BD Biosciences)

TCR beta monoclonal antibody—FITC (H57–597) cat no. 11-5961-86 (Thermo Fisher Scientific)

CD8 Pe-Cy7 (clone SK1, RUO GMP) cat no. 335787 (BD Biosciences)

CD4 PE (clone SK3) cat no. 347327 (BD Biosciences)

CD137 APC (clone 4B4–1, RUO) cat no. 550890 (BD Biosciences)

CD134 FITC (clone ACT35, RUO) cat no. 555837 (BD Biosciences)

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10

Isolation and Phenotyping of Human Immune Cell Subsets

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Peripheral blood samples (10–20 ml) from 20 healthy young adults (13 F/7 M, age range 22–35 years) were collected in heparinized tubes. Peripheral blood mononuclear cells (PBMCs) were isolated by centrifugation of whole blood over a Ficoll-Paque gradient (Biochrom) and washed 4× with ice-cold RPMI1640 culture medium (Gibco). CD19+ B cells, CD14+ monocytes, CD3+ T cells, CD4+ CD25− Th cells, CD4+ CD25+ Th cells, CD8+ T cytotoxic cells, CD4+ CD45RA+ CD25− naive Th cells, and CD4CD45RO+ CD25− memory Th cells were isolated by cell sorting using a BD FACS Aria II flow cytometer (BD Biosciences). The sorting strategy is shown in Figure S1 Supplementary Material. The isolated cell populations were phenotyped and used when their purity reached >95%. The antibodies used for cell sorting and phenotyping were the mouse antihuman monoclonal antibodies (mAbs) CD3-APC-H7 (clone SK7), CD19-APC (clone HIB19), CD14-FITC (clone M5E2), CD4-APC (clone RPA-T4), CD8-FITC (clone HIT8a), CD25-PE (clone M-A251), CD45RA-APC-H7 (clone 5H9), and CD45RO-PE-Cy7 (clone UCHL1) (BD Biosciences), CD25-PC5 (clone B1.49.9) (Beckman Coulter). Fluorescence minus one controls were used to identify any background spread of fluorochromes and establish gating boundaries. The data were analyzed using the BD FACS DIVA software v.8.
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