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8 protocols using anti cd8 sk1

1

PBMC Cell Sorting and Characterization

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Cell sorting was performed from PBMC fractions using FACSAria II (Becton Dickinson) or Sony SH800 (Sony Biotechnology Inc.). For sorting, PBMC cells were stained with anti-CD3 (SK7, BD, cat. no 345767 or 557851), anti-CD4 (SK3, BD, cat. no 345770), anti-CD8 (SK-1, BD, cat. no 335822 or 345772) and the appropriate anti-Vβ antibody. Purities of the sorted cell fractions were controlled with flow cytometry, and the purities were nearly 100%.
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2

Immune Cell Phenotyping under BSL 2+

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Immune cell phenotyping was performed under BSL 2+ conditions by incubating 200 μL of fresh whole blood in polystyrene tubes with two different fluorochrome-labeled antibody panels for 20 min in the dark [Panel 1: anti-CD3 (SP34-2, #562877), anti-CD4 (L200, #560836), anti-CD8 (SK1, #341051); anti-CD19 (HIB19, #555415), anti-CD38 (HIT2, #555460), and anti-HLA-DR (G46-6, #555811) from BD, anti-CD20 (2H7, #47-0209-42) from eBioscience, and anti-CD27 (O323, #302838) from BioLegend. Panel 2: anti-CD3 (UCHT1, #557943), anti-CD11c (O33-782, 561355), anti-CD14 (M5E2, #565283), anti-CD19 (HIB19, #557921), anti-CD123 (7G3, #554529), and anti-HLA-DR (G46-6, #560651) from BD; anti-CD16 (CB16, #47-1068) and anti-CD56 (MEM188, #17-0569) from eBioscience, and anti-CD20 (2H7, #302332) from BioLegend]. Flow cytometry was performed on an LSRII (BD) and data was analyzed using FlowJo software version 9 (Tree Star). T cells expressing both HLA-DR and CD38 were considered activated.
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3

Multiparametric T Cell Immunophenotyping

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Mouse T cells were labeled for 20min at 4°C with anti-CD3 (17A2), anti-CD4 (GK1.5), anti-CD8 (53–6.7), anti-CD45.1 (A20), anti-CD45.2 (104), anti-Vβ5.1–5.2 (MR9–4), anti-CD44 (IM7), anti-CD62L (MEL-14), anti-CD127 (A7R34), KLRG1 (MAFA), anti-IFN-γ (XMG1.2) and anti-TNF-α (MP6-XT22) (all eBioscience). Human T cells were labeled with anti-CD3 (UCHT1, Beckman Coulter), anti-CD4 (SK3, BD Biosciences), anti-CD8 (SK1, BD Biosciences). Dead cells were excluded with 1ng/ml TO-PRO-3 iodide (Sigma-Aldrich), or Near-IR (L10119, Life Technology). Intracellular cytokine staining was performed with the cytofix/cytoperm kit (BD Biosciences). Flow cytometry analysis was performed on LSR-II and LSR Fortessa (BD Biosciences). Data were analyzed with FlowJo software (Tree Star, version 7.6.5 and version 10). Representative flow cytometry gating strategies are found in Fig S9.
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4

Phenotypic Profiling of PBMCs

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PBMCs were washed with PBS plus 2% FBS (Gibco, Grand Island, NY), and then Fc blocking reagent (Miltenyi Biotec, Inc., Auburn, CA) was added, followed by extensive wash. Cells were then incubated for 30 min on ice with anti-CD3 (OKT3) (BioLegend), anti-CD8 (SK1) (BD), anti-CD56 (HCD56) (BioLegend) and live/dead fixable aqua dye (eF660, eBioscience), washed twice with PBS plus 2% FBS and then stored at 4°C until acquired by FACS Verse (BD Biosciences, San Jose, CA). Data were analyzed using FlowJo software (Version 10.0.8, Tree Star Inc., Ashland, Or).
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5

Tetramer-based Enrichment of Antigen-specific CD4+ T Cells

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Untouched CD4+ T cells were isolated from PBMCs using magnetic microbeads (Miltenyi Biotec). Tetramer staining and enrichment was performed as described previously (Su et al., 2013 (link)). In brief, cells were incubated for 30 min with live/dead Aqua marker (Invitrogen), washed, and then labeled with either gE or IE63 tetramers at room temperature for 45 min (14 µg/ml). Surface markers AF700-labeled anti-CD3 (UCHT3; BD), FITC-labeled anti-CD4 (SK3; BD), Pacific blue–labeled anti-CD45RA (MHCD45RA28; BD), and PE-cyanine 7 (PECy7)–labeled anti-CD56 (B159; BD), anti-CD14 (M5E2; BD), and anti-CD8 (SK1; BD) were incubated at room temperature for 15 min. Before tetramer enrichment, 1/10th staining volume was removed and added to TruCount tubes (BD) to give an absolute count of the starting number of CD4+ naive and memory T cells. The remaining staining volume was enriched for tetramer-positive cells using anti-PE microbeads (Miltenyi Biotec) and added to a separate TruCount tube. Samples were acquired using an LSR Fortessa (BD), and the frequency of tetramer-positive cells determined by dividing the absolute counts of tetramer positive cells by the starting number of CD4+ naive/memory T cells.
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6

In Vitro SARS-CoV-2 T Cell Assay

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PBMCs were stimulated with peptide pools and expanded in vitro for 10 days as described before (23 (link)). Expanded T cell lines were stimulated for 5 hours at 37°C with or without SARS-CoV-2 peptide pools (2 μg/mL). After 1 hour, 10 μg/mL brefeldin A (MilliporeSigma) and 1× monensin (BioLegend) were added. Cells were stained with the yellow LIVE/DEAD fixable dead cell staining kit (Invitrogen, Thermo Fisher Scientific) and the surface markers anti-CD3 (SK7 or OKT3; BioLegend), anti-CD4 (SK3, BD Biosciences), and anti-CD8 (SK1, BD Biosciences). Cells were subsequently fixed and permeabilized using the Cytofix/Cytoperm kit (BD Biosciences) and stained with anti–IFN-γ (25723; R&D Systems) and anti–TNF-α (MAb11, BD Biosciences) antibodies and analyzed on a CytoFLEX (Beckman Coulter). Data were analyzed by FlowJo (BD Biosciences).
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7

Cytotoxicity Assay of TRuC/CAR-T Cells

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TRuC or CAR-T cells were co-cultured with one of the following target cells: Raji, RPMI-8226, K562 and Nalm6 cell lines. T cells and target cells were plated at an effector-to-target ratio of 1-to-1 in a 96-well U bottom plate. Anti-CD107a antibody (clone-H4A3) was added to the co-culture for 1 h at 37 °C, 5% CO2. Then, the protein transport inhibitor monensin was added per manufacturer’s instructions and cells incubated for additional 3 h. Subsequently, T cells were labelled with the following antibodies: anti-CD3, (clone UCHT1), anti-CD4 (RPA-T4), and anti-CD8 (SK1) (BD Biosciences, San Jose, CA). Samples were acquired using the BD LSR Fortessa X-20 cell analyzer (BD Biosciences, San Jose, CA) and data analyzed using the FlowJo software (Treestar Inc.).
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8

Entinostat Enhances T Cell Proliferation

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Healthy-donor CD3+ T cells were pretreated overnight with 2.5 µM entinostat+50 U/mL IL-2, controls were treated with 50 U/mL IL-2 only. Cells were subsequently labeled with CellTrace Violet (CTV) and stimulated with 2.5 mg/mL PHA (or left unstimulated). After 72 hours, proliferative capacity was determined by measuring CTV dilution using flow cytometry and additional staining with anti-CD3 AF700 (UCHT1, Sony), anti-CD4 PE (RPA-T4, BD Biosciences), and anti-CD8 (SK1, BD Biosciences) on the BD Fortessa.
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