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7 protocols using ebioscience kit

1

Treg and NK-cell Immunophenotyping

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PBMCs were thawed and stained with either Treg or NK-cell discriminating antibodies. The Treg panel was comprised of the following extracellular antibodies: CD3-AF700, CD4-eFluor780, CD8-PE-Cy7, CD25-PE, CD127-BV421, CD45RO-BV711 (Biolegend, Biolegends, Koblenz; Germany). For intracellular staining, cells were permeabilized after extracellular staining, using the eBioscience kit (Thermo Fisher Scientific, Darmstadt, Germany) and stained for FOXP3 expression. The NK-cell panel comprised of CD3-AF700, CD19-eFluor780, CD56-PE-Cy7, CD16-BV510, CD45RO-BV711, TCRVα24-PE, TCRVβ11-FITC (Biolegend). All samples were measured within 24 h after staining on a BD LSR Fortessa (BD Biosciences, Heidelberg, Germany). All flow cytometry data were analyzed with FlowJo software version 10.6.0 (Tree Star, Ashland, OR, USA). Output CSV documents were further analyzed using RStudio (version 1.2.1335).
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2

Measuring IFN-α in Plasma and PF

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IFN-α in the plasma and PF were measured by enzyme-linked immunosorbent assay (ELISA) using the eBioscience kit (Thermo Fisher, Toronto, ON, Canada) following the manufacturer’s instructions.
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3

Isolation and Characterization of Lymphocytes from Colon Tissues

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Tumor and spleen tissues were collected for lymphocyte isolation. The colon was cut longitudinally, washed with PBS, and 1–2 cm of colon tissue surrounding the tumor was excised. After removing epithelial cells and the mucus with solution A [50 mL of PBS, 3 mL of 0.5 mM EDTA, 500 μL of 1 M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), and 25 μL of 2 M dithiothreitol (DTT)], the colon tissue was transferred to a new centrifuge tube. After addition of solution B (50 mL of PBS, 3 mL of 0.5 mM EDTA, and 500 μL of 1 M HEPES), the colon tissue was digested with 1 mg/mL collagenase VIII (Sigma–Aldrich), followed by filtration and resuspension of the cell precipitate in a 40% Percoll solution. Next, the cell precipitate was washed with 80% Percoll and resuspended in PBS to obtain a single-cell suspension. The cells were incubated with antibodies (Supplementary Table S4) and stained with propidium iodide. Flow cytometry was performed using an LSRFortessa X-20 flow cytometer (BD Biosciences, Franklin Lakes, NJ, USA). Single-cell suspensions from spleen tissue were prepared and analyzed using the same method. CD4+CD25+FOXP3+ and other cell populations were characterized using an eBioscience kit (eBioscience, San Diego, CA, USA).
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4

Cytotoxicity and Viability Assays for Drug Screening

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Cells were plated at a density of 1 × 104 cells/well in 96-well plate overnight, and treated with BLM (10, 50, 100 and 200 μg/ml) for 24 h. Cells were stimulated with LPS (10 ng/ml) or SNP (10 μM) during the last 18 h of treatment with BLM. At the end of the treatment period, 50 μl of 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) solution (0.5 mg/ml) was added to each well and the plate incubated for 3 h. The supernatant was aspirated, and the formazan crystals formed, solubilized in 200 μl DMSO for 30 min. The extent of reduction of MTT to formazan within cells was quantified by multimode plate reader at 550 nm (VarioSkan Flash, Thermo Fisher Scientific, Finland). In another experiment, designed to assess the viability, LPS-stimulated cells (1 × 104) were stained with calcein (AM) and/or propidium idodide (5 μl for 100 μl of culture medium with 1 × 104 cells) in 1 ml staining buffer and incubated for 30 min at room temperature as per manufacturers’ protocol (Affymetrix, Ebioscience kit). They were washed two times with staining buffer, and the cells were read in Flow Cytometer, Cell Lab Quanta SC™ flow cytometer (Beckman Coulter) as per manufacturers’ protocol.
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5

Multiparametric flow cytometry analysis

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Cells were stained with the live/dead marker Aqua (Thermo Fisher Scientific) and fixed with the eBioscience Foxp3/Transcription Factor kit or with 1.9% paraformaldehyde (Sigma-Aldrich). For the surface staining of the degranulation marker CD107a, cells were left unfixed and directly processed for flow cytometric analysis. For intracellular staining, cells were permeabilized with the eBioscience kit or 0.5% saponin (Sigma-Aldrich). Flow cytometric analysis was performed by staining with fluorochrome-labeled antibodies against mouse CD3, CD19, CD44, CD45RB, CD107a, CTLA-4, F4/80, Foxp3, GzmB, IL-10, IL-12p40, MHCII, TNF (all eBioscience), CD11c, CD25, IFN-γ (BD Biosciences), and CD8, CD64, GITR, PD-1 and PD-ligand 1 (Biolegend, Uithoorn, NL). For all flow cytometric stainings, FcγR-binding inhibitor (2.4G2) was added and fluorescence minus one (FMO) controls were used for gate setting. Flow cytometry was performed using a FACSCanto (BD Biosciences).
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6

Cytokine and Mucin Quantification

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For cell culture experiments, supernatants were collected 24 h after the second HDM dose and used to assess secreted levels of IL8, IL6, CCL20, and G-CSF (DuoSet ELISA Kits, R&D Systems, Minneapolis, MN, USA) per the manufacturer’s instructions. For mouse experiments, right side lung lobes were flash frozen immediately after harvest and crushed to make lysates in buffer containing 137 mM Tris-HCL (pH 8.0) 130 mM NaCl, and 1% NP-40. Samples were normalized to total lung protein and used to assess expression levels of IL5, IL6, IL33, CXCL1, Eotaxin-1 (DuoSet ELISA Kits, R&D Systems, Minneapolis, MN, USA), IL4, IL13 (eBioscience Kits, Thermo Fisher Scientific, Waltham, MA, USA), and MUC5AC and MUC5B (Novus Biologicals, Littleton, CO, USA) per manufacturer’s instructions.
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7

Quantifying Lung Inflammatory Mediators

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Right side lung lobes were flash frozen immediately after harvest and crushed to make lysates in buffer containing 137 mM Tris HCl (pH 8.0), 130 mM NaCl, and 1% NP-40. Samples were normalized to total lung protein and used to assess the abundance of IL-6, IL-33, CCL20, Eotaxin-1 (DuoSet ELISA Kits, R&D Systems, Minneapolis, MN, USA), IL-4, IL-13 (eBioscience Kits, Thermo Fisher Scientific, Waltham, MA, USA), and MUC5AC (Novus Biologicals, Littleton, CO, USA) per manufacturer's instructions.
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