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20 protocols using cd3 percp cy5

1

Multiparameter Tumor Immune Profiling

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Single cell suspensions of collagenase-digested tumors were stained with the following antibodies purchased from eBioscience: fixable viability dye efluor 450, CD69-FITC, PD-1-PE, CD4-PeCy7, CD45-Alexa Fluor 700, CD8a-PE efluor 610, CD40-FITC, CD70-PE, MHC-II IAd-APC, CD11c-PE efluor 610, CD45-APC, CD3-PerCP-Cy5.5, CD11b-PerCP-Cy5.5, EpCAM-PeCy7, PD-L1-PE and PD-L2-FITC. Phospho-Smad2/3 levels were assessed as previously described (27 (link)). Briefly, TDLN cells were stained with anti-mouse CD4-PE and anti-mouse CD8-FITC (eBioscience), fixed, permeabilized (Foxp3 Fixation/Permeabilization Concentrate and Diluent kit, eBioscience) and stained with goat anti-phospho-Smad2/3 (Ser 423/425) followed by APC-labeled donkey anti-goat IgG (Santa Cruz Biotechnology). All samples were acquired with LSRII flow cytometer and analyzed with FlowJo software (version 7.3.6).
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2

Isolation and Characterization of Murine CD4+ T Cells

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Naïve CD4+ T cells were isolated from spleens of wild-type C57BL/6 J mice (8–14 weeks; both sexes). In brief, dissected mouse spleens were gently ground through 70 µm cell strainer mesh (Falcon), and naïve CD4+/CD25+ (regulatory; Treg) or CD4+/CD25- (effector; Teff) T cells were isolated and collected using a CD4+CD25+ T cell isolation kit (Miltenyi Biotec; #130-091-041) and magnetic separation columns (Miltenyi Biotec, #130-042-201 and #130-042-401) according to manufacturer’s protocol. Purity of T cell populations were verified by using flow cytometry (Supplementary Fig. 6a; CD3-PerCP-Cy5.5 1:100, eBioscience, #45-0031-80; CD4-Pacific Blue 1:100, eBioscience, #57-0042-82; and Foxp3-APC 1:100, eBioscience, #17-5773-80; FlowJo v.10.6.2). Isolated CD4+ T cells were resuspended in RPMI 1640 containing 10% FBS, 1% PSQ, 1% sodium pyruvate, 1% HEPES, and 1% nonessential amino acids, and plated on poly-L-lysine coated coverslips >1 h before recording. Whole-cell recording of CD4+ T cells was carried out within 48 h after isolation.
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3

PBMC Processing and CD4+ T Cell Enrichment

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PBMC sample processing was performed at the same time for each triplet (PwMS at VIS1&VIS2 and HC), to minimize differences within processing. The MojoSort™ Human CD4 T Cell Isolation Kit (#480010, BioLegend, San Diego, CA, USA) was used for CD4+ T cell enrichment, in accordance with the manufacturer’s instructions.
To assess whether CD4+ T cell enrichment was achieved, flow cytometry was performed in a BD LSRFortessa™ X-20 Cell Analyzer (BD Biosciences, Franklin Lakes, NJ, USA) on a subset of samples (before and after magnetic enrichment). The following antibodies were used: CD14-eFluor450 (#48014941, clone 61D3, eBioscience™, Thermo Fisher Scientific, Waltham, MA, USA); CD19-Alexa Fluor 647 (#302222, clone HIB19, BioLegend, San Diego, CA, USA); CD3-PerCP-Cy5.5 (#45003741, clone OKT3, eBioscience™, Thermo Fisher Scientific, Waltham, MA, USA); CD4-BV711 (#317439, clone OKT4, BioLegend, San Diego, CA, USA); and CD56-PE-Cy7 (#25056741, clone CMSSB/NCAM, eBioscience™, Thermo Fisher Scientific, Waltham, MA, USA).
Regarding the gating strategy, CD4+ T cells were defined as CD3+CD4+CD19-CD56- single cells (see Supplementary Figs. S6, 7 online). A detailed protocol and additional details regarding the methodology used for CD4+ T cell enrichment and flow cytometry may be found in Sect. 2 of the Supplementary Information.
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4

Multiparameter Immune Cell Profiling

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CD3-percp-cy5.5 (Catalogue #45-0036-42), CD8-APC (Catalogue #17-0086-42), CD8-FITC (Catalogue #11-0086-42), CD14-APC (Catalogue #17-0149-42), CD56-FITC (Catalogue #4278380), CD16-PerCP-eFluor™710 (Catalogue #46-0168-42), CD11b-PerCP-eFluor™710 (Catalogue #46-0110-80), IFN-γ-PE (Catalogue #12-7319-42), TLR2-FITC (Catalogue #11-9922-41) and Mouse IgG1-PE (Catalogue #12-4714-81) were all bought from eBioscience. HLA-DR-PE (Catalogue #555812), IL-10-APC (Catalogue #554707), CXCR3-APC (Catalogue #550967) and IFN-γ-FITC (Catalogue #561053), Rat IgG2a-APC (Catalogue #554690) and mouse IgG-APC (Catalogue #5065947) were purchased from BD Biosciences. CD16-FITC (Catalogue #302006), HLA-DR-APC (Catalogue #307609), CD3-FITC (Catalogue #317306) and TLR4-APC (Catalogue #312815) were purchased from Biolegend. EP2-PE (Catalogue #10477) and Rabbit IgG-PE (Catalogue D5-1610) were purchased from Cayman Chemical.
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5

Multiparameter Flow Cytometry Analysis

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Single-cell suspension cells were incubated with the respective conjugated antibody for 15 min at 4 °C and analyzed with a BD LSR. IgM-APC (catalog: 551062) was from BD Biosciences. CD19-FITC (catalog: 11-0199), CD45-Alexa Fluor 700 (catalog: 56-9459), CD3-PerCP-Cy5.5 (catalog: 45-0037) and CD34-PE-Cyanine 7 (catalog: 25-0349) were from eBioscience. CD38- PerCP-Cy5.5 (catalog: B49199), TDT-PITC (catalog: IM3524), CD22-PE (catalog: IM1835U), CD5-PerCP-Cyanine 5.5 (catalog: B49191), CD19-ECD (catalog: 652804), CD10-PE (catalog: A07760) and CD34-ECD (catalog: IM2709U) were from Beckman Coulter. Propidium iodide were from Sigma. The gating strategy for MCL cells were selected using CD19/IgM, CD19/IgM+ and CD19+/IgM+cells (gate i: CD45+/PI; gate ii: CD34/CD3; gate iii: CD19/IgM, CD19/IgM+ and CD19+/IgM+). The sorting purity was greater than 99% in the majority of samples. All the fractions were isolated by fluorescence-activated cell sorting (Aria, Becton Dickinson, San Jose, CA).
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6

Quantitative Analysis of Myeloid-Derived Suppressor Cells and T-Cells in Tumor Samples

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To characterize and quantify MDSCs by FACS, cells were incubated with FcR blocker (eBioscience), then stained with Ly6C-PE-CF594 (BD Biosciences), Ly6G-PerCPCy5.5 (BD Bioscience), CD11b-APC (eBioscience) and/or anti-GR1 (RB6, BD Biosciences). MDSCs were identified as GR1+CD11b+ cells, granulocytic MDSCs as Ly6GhighLy6Clow or −CD11b+, monocytic MDSCs as Ly6ChighLy6GlowCD11b+. To determine absolute cell numbers counting beads (BD Biosciences) were added before FACS acquisition. T-cells were analyzed with an antibody combination of CD3-PerCPCy5.5, CD4-APC, CD8-FITC (all eBioscience) and PD1-PE-CF594 (BD Biosciences). Please also see Supplementary Table 2 for antibody use information.
Tumor infiltrating MDSCs and T-cells were quantitated by enzymatic digestion of the dissected tumors (Mouse tumor cell dissociation kit, Miltenyi Biotec), followed by FACS staining with the above antibody combinations. Staining for the common leukocyte marker CD45 was also included to facilitate the distinction of leukocytes from tumor cells and other stromal cells.
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7

Lung Cell Dissociation and Characterization

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The left lung lobe of each sample was dissociated in RPMI 1640 medium containing type IV collagenase (MP Biomedicals) and DNase I (Spectrum) using gentleMACS C tubes according to the manufacturer’s recommendations (Miltenyi Biotec). Cells were filtered through a 70-μm strainer, and red blood cells were lysed before blocking Fc receptors using anti-CD16/CD32 (BioLegend). Cell-specific proteins were labeled with CD11b-Alexa Fluor 488 (eBioscience), Ly6G-allophycocyanin (APC) (eBioscience), CD64-phycoerythrin (PE) (BioLegend), or SiglecF-peridinin chlorophyll protein (PerCP)-Cy5.5 (BD Biosciences) antibody or the appropriate isotype control antibodies. T cell subsets were stained with antibodies against CD3-PerCP-Cy5.5 (eBioscience), CD8-APC (eBioscience), and CD4-Alexa Fluor 488 (BioLegend). Stained cells were incubated in BD stabilizing fixative (BD Biosciences) and analyzed using a FACSAria cytometer (BD Biosciences). Results were analyzed using FlowJo software (TreeStar), and gating was performed based on fluorescence-minus-one controls. The gating strategy used to identify neutrophils, alveolar macrophages, and interstitial macrophages is shown in Fig. S7 in the supplemental material. T cells were gated as CD3+/CD4+ T helper cells and CD3+/CD8+ cytotoxic T cells.
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8

Profiling PD-1+ T Cells in PD-1 Therapy

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We collected whole blood samples of 6 patients before PD-1 antibody treatment at indicated cycles, 1-2 (weeks 3-6). Peripheral blood mononuclear cell (PBMC) samples were isolated by density-gradient centrifugation using lymphoprep (MD pacific, Tianjin, China) and cryopreserved. Before conducting flow cytometry, the PBMC samples were thawed, washed twice with phosphate buffer saline and incubated with antibodies for surface markers including CD3 PerCP-cy5.5 (eBioscience), CD4 APC-eFlour780 (eBioscience), CD8-FITC (eBioscience), and PD1-APC (eBioscience), followed by staining, for intracellular marker, with Ki67 (Biolegend). The mixture of surface marker antibodies were incubated with the PBMC samples for 30 min at room temperature in the dark. Permeabilization was performed using the FOXP3/Transcription Factor Staining Buffer Set (eBioscience). Stained cells were suspended in an appropriate volume of flow cytometry staining buffer until data acquisition. A BD Bioscience LSR Fortessa X-20 instrument was used to acquire data of the stained samples, which was further analyzed using the FlowJo software.
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9

Liver Macrophage Phenotyping in Mice

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Liver tissues from male C57BL/6J mice were minced and digested for 30 min at 37 °C with type II collagenase (Sigma-Aldrich) in PBS containing 2% BSA (pH 7.4). The cell suspension was filtered and then spun at 3000 rpm for 5 min to separate the floating liver tissue fraction from the stromal vascular cell (SVC) pellet. The SVCs were resuspended in PBS supplemented with 2% FBS and incubated with Fc-Block (BD Bioscience).
To determine macrophage phenotype fluorescence-activated cell sorting analysis FACSAriaII (BD Bioscience) was performed using following antibodies, NK1.1-PerCP Cy5.5 (eBioscience, San Diego, CA), CD3-PerCP Cy5.5 (eBioscience, San Diego, CA), CD19-PerCP Cy5.5(eBioscience), TER119-PerCP Cy5.5 (eBioscience, San Diego, CA), CD45-APC-Cy7(eBioscience, San Diego, CA), Gr-1Fluor450 Ly-6G(PB) (eBioscience, San Diego, CA), F4/80-PE-Cy7(Bio Legend, San Diego, CA), CD11b-PETR (Invitrogen, Carlsbad, CA, USA), CD11c-PE(eBioscience, San Diego, CA), CD206 Alexa Fluor 647 (Bio Legend, San Diego, CA). Data analysis and compensation were performed using FlowJo (Tree Star).
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10

PBMC and Gastric Tissue Immunophenotyping

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PBMC and gastric tissue cell suspension were stained for various surface markers: Live/dead-PE-CF594 (BD Biosciences, San Jose, CA, USA), CD45-AF700 (Invitrogen, Grand Island, NY, USA), CD3-Percpcy5.5 (eBiosciences, San Diego, CA, USA), CD4-FITC (eBiosciences), CD8a-APC-eF780 (eBiosciences), and PD-1/isotype-APC (BD Biosciences). Samples were analyzed with a BD LSRFortessa X-20.
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