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6 protocols using anti ccr7

1

Comprehensive Immune Cell Profiling by Flow Cytometry

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The following antibodies were used for flow cytometry analysis: anti-IFNγ (XMG1.2, 1:50), anti-CD45.1 (A20, 1:100), anti-CD45.2 (104, 1:100), anti-IL1β-APC (NJTEN3, 1:50), anti-CD44 (IM7, 1:100), anti-CD62l (MEL-14, 1:100), anti-F4/80 (BM8, 1:100), anti-CCR7 (4B12, 1:100), anti-CD4 (RM4-5, 1:200), anti-CD8α (53-6.7, 1:200), anti-H-2Kb (AF6-88.5.5.3, 1:200), anti-Ly6G (RB6-8C5, 1:100), anti-MHC class II (I-A/I-E) (M5/114.15.2, 1:100) and anti-CD11c (N418, 1:100) were from eBioscience. Anti-CD103 (2E7, 1:100) was from Biolegend. Annexin V apoptosis Detection kit (556547) was from BD Pharmingen. For intracellular cytokine staining, Cytofix/Cytoperm plus kit (BD, cat. 55508) was used. For Foxp3 staining, Foxp3 staining buffer set (eBioscience, cat. 00-5523-00) was used. Multiple-colour flow cytometric analysis was performed using FACSAria (BD Biosciences; Franklin Lakes, NJ, USA). For FACS sorting, cells stained with FACS
antibodies were sorted on BD FACSAria device. FlowJo software was used for data acquiring and analysis.
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2

Isolation and Proliferation of Human CD4+ T Cells

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Buffy coats were obtained from healthy donors who gave informed consent. Peripheral blood mononuclear cells (PBMCs) were isolated using Lympholyte (Cederlane, CL5020) density gradient separation. CD4+ T cells were MACsorted from PBMCs using human anti‐CD4 magnetic beads (Miltenyi Biotech, 130–045–101), stained with carboxyfluorescein succinimidyl ester (CFSE; Life Technologies, C34554). and plated in RPMI Medium 1640 (Gibco, A10491‐01) supplemented with 10% FBS, 1% penicillin/streptomycin, 1% Minimum Essential Medium Nonessential Amino Acid (MEM‐NAA; Gibco, 11140–035) and 0.1% 2‐mercaptoethanol. For stimulation, T cells were incubated with anti‐CD3/anti‐CD28 beads (Dynabeads Human T‐Activator, Gibco, 11131D) for 5 days. T cell proliferation was measured by flow cytometric CFSE dilution assay using LSRII Fortessa analyzer. T cell phenotype was assessed using anti‐CD45RA, anti‐CD45RO, anti‐CCR7, and anti‐CD27 antibodies (all from eBioscience).
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3

Multicolor Flow Cytometry Panel for Immune Profiling

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Cells were stained with the following antibodies obtained from BD Biosciences (Franklin Lakes, NJ, USA), eBioscience, or BioLegend (San Diego, CA, USA): anti-CD4 (BioLegend, 100451), anti-CXCR3 (eBioscience, 12-1831-82), anti-CCR7 (eBioscience, 12-1971-82), anti-CD44 (eBioscience, 12-0441-83), anti-CD62L (BioLegend, 104406), anti-CD11c (BD Bioscience, 553801), anti-MHCII (BioLegend, 107631), anti-CD80 (BD Biosciences, 553769), anti-CD86 (BD Biosciences, 553692), anti-B220 (eBioscience, 12-0452-83), anti-CD8 (BD Bioscience, 553032), anti-CD103 (BD Bioscience, 557495), anti-CD45 (BioLegend, 103132), and anti-CD11b (BioLegend, 101263). For Th1 and Treg analyses, cells were stained for surface markers, permeabilized with the Intracellular Fixation and Permeabilization Buffer Set (eBioscience, 88-8824-00), and then stained with anti-IFN-γ (BioLegend, 505825) and anti-FOXP3 (eBioscience, 17-5773-82) antibodies. The following antibodies were obtained from Cell Signaling Technology (Danvers, Massachusetts, USA): anti-Ezh2 (#5246), anti-Runx1 (#4336), and anti-H3K27me3 (#9733). The Alexa Fluor™ 488 Goat Anti-Rabbit SFX Kit from Invitrogen (Carlsbad, CA, USA) was used as a secondary antibody. Multicolor flow cytometric analysis was performed using a CytoFLEX LX (Beckman Coulter, Indianapolis, IN, USA).
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4

Characterization of Senescent and Exhausted T Cells

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PBMCs were isolated using Ficoll-Paque (GE Healthcare, USA), and the cellular phenotypic of senescent and exhausted T cells was analyzed by flow cytometry. For surface markers analysis, cells were stained in PBS containing 2% fetal bovine serum (FBS, Thermo fisher, USA) with antibodies as indicated. Then, flow cytometric analysis was carried out in BD LSRFortessa X20. The gating strategy to identify T cell subsets was applied as described previously (27 (link)). Antibodies used in this study were purchased from BD Biosciences and eBioscience, including anti-CD4 (GK1.5, 1:100), anti-CD8 (53-6.7, 1:100), anti-CD25 (PC61, 1:100), anti-CD45RA (HI100, 1:100), anti-CXCR3(G025H7, 1:100), anti-CCR4 (L291H4, 1:100), anti-CCR6 (G034E3, 1:100), anti-CCR7 (G043H7, 1:100), anti-CD127 (A019D5, 1:100), anti-CXCR5 (RF8B2, 1:100), anti-CD28 (CD28.2, 1:100), anti-CD57 (NK-1, 1:100), anti-KLRG1 (2F1, 1:100), anti-PD-1 (EH12.2H7, 1:100), anti-TIM3 (F38-2E2, 1:100), and fixable viability dye eFluor 780 (eBioscience, Cat#65-0865-14, 1:1,000).
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5

Isolation and Sorting of CD8+ T Cell Subsets

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Peripheral blood mononuclear cells (PBMCs) were obtained from healthy donors by density gradient centrifugation with Lymphoprep (AXIS-SHIED Rodelokka, Oslo, Norway). CD3+ and CD8+ lymphocytes were isolated by a magnetic-activated cell sorter (MACS) using CD3 Microbeads and a CD8 T cell isolation kit (MiltenyiBiotec), respectively. The cells were then labeled with anti-CD8, anti-CCR7, and anti-CD45RA (Ebiosciences) and sorted into naïve and memory CD8+ T cell subsets on a BD fluorescence activated cell sorting (FACS) Aria sorter (BD Biosciences). For extraction of TILs, tissue from lung tumor samples were minced and digested with collagenase (2.5 mg/ml collagenase I) at 37 °C for one hour. Cell suspension was then twice filtered through 100-μm and 40-μm cell strainers (BD Biosciences) to obtain single cells. TILs were isolated from single cells utilizing density gradient centrifugation with Lymphoprep and further purified using CD8 MicroBeads (MiltenyiBiotec).
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6

Phenotypic Analysis of Senescent and Exhausted T Cells

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Peripheral blood mononuclear cells (PBMCs) were isolated using coll-paque (GE Healthcare, USA) for cellular phenotypic analysis of senescent and exhausted T cells by ow cytometry. For analysis of surface markers, cells were stained in PBS containing 2% fetal bovine serum (FBS, Thermo sher, USA)
with antibodies as indicated. Then ow cytometric analysis was carried out in BD LSRFortessa X20. The gating strategy to identify T cell subsets was applied as described previously 28 . Brie y, markers related to T cell senescence and exhaustion were also monitored using PD-1 TIM3 CD28 and CD57 antibodies.
Antibodies used in this study were from BD Biosciences and eBioscience, including anti-CD4 (GK1.5, 1:100), anti-CD8 (53-6.7, 1:100), anti-CD25 (PC61, 1:100), anti-CD45RA (HI100, 1:100), anti-CXCR3 (G025H7, 1:100), anti-CCR4 (L291H4, 1:100), anti-CCR6 (G034E3, 1:100), anti-CCR7 (G043H7, 1:100), anti-CD127 (A019D5, 1:100), anti-CXCR5 (RF8B2, 1:100), anti-CD28 (CD28.2, 1:100), anti-CD57 (NK-1, 1:100), anti-KLRG1 (2F1, 1:100), anti-PD-1 (EH12.2H7, 1:100), anti-TIM3 (F38-2E2, 1:100).
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