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53 protocols using live dead near ir

1

HLA-DP-expressing Jurkat reporter assay

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HLA-DP-expressing Jurkat E6.1 cells were co-incubated with NKp44ζ+, NKp46ζ+ Jurkat reporter cells or untransduced Jurkats at an effector to target ratio of 1:10 for 5 h at 37 °C/5% CO2. For peptide-pulsing experiments, HLA-DP-expressing Jurkat E6.1 cell lines were washed twice with serum-free medium and pulsed with 100 µM CLIP peptide (sequence: LPKPPKPVSKMRMATPLLMQALPM; GenScript) or an equivalent amount of DMSO for 18 h at 37 °C/5% CO2. After peptide pulsing, JE6.1-DP cells were washed and co-incubated with Jurkat reporter cell lines. Subsequently, cells were stained with anti-CD3-BUV737 (BD Biosciences), anti-NKp44-PE (Biolegend) or anti-NKp46-PE (BD Biosciences), anti-CD69-BV421 (Biolegend), LiveDead NearIR (Life Technologies) and anti-HLA-ABC-APC (Biolegend), to discriminate between HLA-DP-expressing JE6.1 and Jurkat reporter cells, for 30 min at 4 °C. Cells were fixed with 4% PFA and analyzed on a BD LSR Fortessa. HLA-DP and CLIP surface expression of JE6.1-DP cells was assessed by staining CLIP-pulsed and DMSO-pulsed JE6.1-DP cells with anti-CD3-BUV737 (BD Biosciences), anti-HLA-DP-APC (Leinco Technologies), anti-CLIP-FITC (BD Biosciences) and LiveDead NearIR (Life Technologies) for 30 min at 4 °C. Cells were subsequently fixed and analyzed on a BD LSR Fortessa. (A detailed list of antibodies used is displayed in Supplementary Table 2.)
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2

Multiparameter Flow Cytometry for Immune Cell Analysis

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Cell suspensions were stained with Near-IR LIVE/DEAD™ (Life Technologies), CD3-PC5 or CD19-PC5, and CD11b-PE when indicated (BD Biosciences). Samples were acquired on a FORTESSA cytometer (BD Biosciences). Data were exported and analyzed with FlowJo (RRID : SCR_008520; version 9-2, MacOS X). Counting beads and cells were gated on forward scatter-area/side-scatter area- (FSC-A/SSC-A) (shown in Figure 1C). Doublets were excluded on FSC-A/FSC-H. Dead cells were excluded on the expression of the viability dye (shown in Figure S1A). PMNs were gated as SSChi cells and CD11b expression. For analysis of trogocytosis of PMNs, target T cells were excluded on the expression of CD3. For cytotoxicity assays, targets (T cells, Jurkat T cell-lines, and Raji B lymphoma cell-line) were gated on SSClowFSChi, cell-trace, and CD3 or CD19 expression.
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3

Evaluating Anti-Tumor Reactivity of TILs

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Anti-tumor reactivity of in vitro expanded TILs was evaluated after co-culture of the TILs with autologous tumor cell lines pretreated with 100 IU/ml IFN-γ (Peprotech, 300-02-100UG) in a ratio of 3:1 for 5 hours. Golgi plug (BD Biosciences, 51-2301KZ) and BV421 CD107a were added at the beginning of incubation and TILs were stained with Near-IR Live/Dead (Life Technologies, L10119) and for surface markers FITC CD3, PE CD56, QDot605 CD8 and PerCP CD4. Subsequently, the cells were fixed and permeabilized (eBioscience, 00-5123-43, 00-5223-56 and 00-8333-56) overnight and stained for intracellular cytokines APC TNF and PE-Cy7 IFN-γ. The manufacturer information and clones of the flow cytometry antibodies are listed in Supplementary Table S4. The TILs were analyzed with a FACS Canto II. Tumor-reactive TILs were defined as T cells expressing either TNF, IFN-γ or CD107a. The response in an unstimulated sample (negative control) was subtracted from the stimulated samples. The gating strategy is shown in Supplementary Fig. S8.
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Phenotyping IFN-γ-Primed Tumor-Infiltrating Lymphocytes

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Tumor cells were either pretreated with IFN-γ (100 IU/mL, Peprotech) or left untreated for 3 days. TILs were then added in a 1:1 ratio, with protein transport inhibitors brefeldin A (1:1000 dilution, GolgiPlug, catalog 555029, BD), Monensin (1:1000 dilution, GolgiStop, catalog 554724, BD), and anti–CD107a-BV421 antibodies (clone H4A3, BD 562623). Tumor cells and TILs were cocultured for 5 hours, after which all cells were stained with Near-IR LIVE/DEAD (Life Technologies) and for surface markers CD3-FITC (clone SK7, BD 345764), CD8-QDot605 (clone 3B5, Thermo Fisher Q10009), and CD4-BV711 (clone SK3, BD, catalog 563028). Subsequently, the cells were fixed and permeabilized (eBioscience) overnight and stained for intracellular cytokines TNF-APC (clone MAb11, BD catalog, 554514) and IFN-γ–PE-Cy7 (clone B27, BD, catalog 557643). Cells were analyzed on a Novocyte Quanteon (ACEA Biosciences). See details related to antibodies used in Supplemental Table 2.
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5

Murine B Cell and Tfh Immunophenotyping

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For immunophenotyping of murine B cells and Tfh cells, spleens from immunized mice one week after the third immunization were processed into single-cell suspensions and treated with ACK lysis buffer to remove red blood cells. Splenocytes (2 × 106) were suspended in 100 μL PBS/2% FBS. To detect antigen-specific B cells, fluorochrome-mAb conjugates and fluorochrome-conjugated CH848 10.17DT Envs were prepared as a master mix at 2× concentration, then 100 μL of 2× master mix was added to an equal volume of cells (Figure S4). Staining for T cell subsets was conducted in the same manner, with the additional step for detection of biotinylated mAb with Streptavidin–APC. Cells were incubated at 4°C for 20 minutes, then washed with PBS. Cells were resuspended in 100 μL PBS containing Near-IR Live/Dead (Thermo Fisher Scientific) at 1:1000, and incubated at room temperature for 20 min. Cells were washed in PBS/2% FBS, then re-suspended in PBS/2% formaldehyde. Cells were analyzed on a BD LSRII (BD Biosciences). Data were analyzed using FlowJo v10 (FlowJo).
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6

OPC Expansion with bFGF Modulation

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Primary cultures of OPCs derived from neonatal rats were expanded and reseeded 500,000cells/well in a 48-well plate. Settled cells were cultured with 10 µM EdU for 72h in media containing Neurobrew, N2 and PDGF-BB as described above. In addition, media was supplemented with full (1/1), half (1/2) of absent (0) of bFGF concentration referred to the concentration described above. Cells were harvested with Accutase, labeled with anti-PDGFRα (Milteny Biotec, Bergisch, Germany). Dead cells were excluded using near IR Live/Dead (Thermo Fisher Scientific, Waltham, MA). Samples were analyzed with a 3-laser Beckman Coulter Gallios using Kaluza Software (Beckman Coulter, Brea, CA).
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7

Isolation and Analysis of Brain Tumor Cells

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Single-cell suspensions of brain tumors were generated by gentle mechanical disassociation followed by enzymatic disassociation. The enzymatic solution (EZ) is as follows: 32 mg collagenase IV (Worthington), 10 mg deoxyribonuclease I (Worthington), 20 mg soybean trypsin inhibitor (Worthington), resuspended in 10 mL of PBS. Enzymatic disassociation took place in 500 μL of EZ for 30 min shaking at 37°C. Following disassociation, cells were passed through a 70 μM filter (Fisher), then washed with PBS. Cells were then stained with fluorescently conjugated antibodies for flow cytometry. Antibodies used include: Near IR LIVE/DEAD (Thermo Scientific); CD45 (30-F11), LY6C (HK1.4), CD8 (53-6.7), CD4 (GK1.5), CD11c (N418), NK1.1 (PK136), CD38 (90), CD103 (2E7), and CD279 (29F.1A12) (Biolegend); and CD11b (M1/70), LY6G (1A8), CD3 (17A2), and CD4 (RM4-5) (BD Biosciences). Total cell counts were determined using CountBright Absolute Counting Beads (Invitrogen). Data were collected using either a BD LSRII or a BD Accuri c6 Plus. Data were analyzed using FlowJo version 10.3.
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8

Murine Lymphocyte Immunophenotyping Protocol

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For immunophenotyping of murine B cells and Tfh cells, spleens from immunized mice one week after the third immunization were processed into single-cell suspensions and treated with ACK lysis buffer to remove red blood cells. Splenocytes (2×106) were suspended in 100 μL PBS/2% FBS. To detect antigen-specific B cells, fluorochrome-mAb conjugates and fluorochrome-conjugated CH848 10.17DT Envs were prepared as a master mix at 2x concentration, then 100 μL of 2x master mix was added to an equal volume of cells (Figure S4). Staining for T cell subsets was conducted in the same manner, with the additional step for detection of biotinylated mAb with Streptavidin–APC. Cells were incubated at 4°C for 20 minutes, then washed with PBS. Cells were resuspended in 100 μL PBS containing Near-IR Live/Dead (Thermo Fisher Scientific) at 1:1000, and incubated at room temperature for 20 min. Cells were washed in PBS/2% FBS, then re-suspended in PBS/2% formaldehyde. Cells were analyzed on a BD LSRII (BD Biosciences). Data were analyzed using FlowJo v10 (FlowJo).
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9

Antibody-Dependent Cellular Cytotoxicity and Phagocytosis Assays

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The ADCC and ADCP assays are also modifications of the CBA in combination with previously established flow cytometry-based ADCC (48 (link)) and ADCP assays (87 (link), 88 (link)). In this case, serum (1:10) or mAbs (1μg/mL unless otherwise indicated) were added to 5,000 MOG-GFP transfected HEK cells plated in 96-well round-bottom plates and incubated for 15 minutes at room temperature. All serum samples were HI prior to use to inactivate endogenous complement proteins. Then, effector cells were added at a 10:1 effector/target ratio. For the ADCC assay, the effector cells were NK cells that were magnetically isolated (EasySep Human NK Cell Isolation Kit, STEMCELL Technologies) from pooled HD-derived cryopreserved PBMCs. The effector cells for the ADCP assay consisted of the THP-1 macrophage cell line (ATCC), labeled with CellTrace Violet (Thermo Fisher Scientific). After addition of the effector cells, the plates were then incubated at 37°C for 4 hours and shaken intermittently. For the ADCC assay, the cells were then stained with Near IR Live/Dead (Invitrogen) stain for 30 minutes on ice, to identify killed target cells. MOG+ and MOG were detected as in the CBA as GFP+. For the ADCP assay, macrophages were identified in the V450 channel and phagocytosis of MOG+ cells in the GFP channel. Data were normalized to the mean media-only condition (no antibodies or serum).
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10

Characterization of Hematopoietic Stem Cells

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After each treatment, cells were washed with ice-cold FACS buffer (PBS with 0.5% FBS) and then stained for 15 min at 4 °C in FACS buffer containing antibodies against human CD34 (BD Biosciences), CD38(BD Biosciences), Lineage cocktail (BD Biosciences), CD123(BD Biosciences), CD90, (BD Biosciences), CD45(BD Biosciences), and Near IR live dead (Invitrogen). The measurements of intracellular proteins were assayed per the Fix Perm kit (BD Biosciences) and stained for RPL5 (ImageBio). For measurement of ROS, CellRox (Invitrogen) was used to measure per manufacturer's protocol. Stained cells were analyzed immediately on a FACS Celesta cytometer (BD Biosciences). In order to isolate specific subpopulations, the cells were stained as above and a FACS Aria II (BD Biosciences) was used to viably sort cells for further assays. Data were analyzed and prepared via FlowJoTM (Treestar).
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