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12 protocols using lipopolysaccharide lps

1

Holi Colour Exposure on PBMCs

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Blood was withdrawn under authorised supervision from six healthy donors who had given their informed consent. PBMCs were isolated from lithium heparin anti-coagulated blood by Ficoll-Paque™ Plus (GE Healthcare Bio-Sciences AB, Uppsala, Sweden) density gradient centrifugation and resuspended in VLE RPMI 1640 (Very Low Endotoxin) media (Biochrom AG, Berlin, Germany) supplemented with 10 % (v/v) FCS (Fetal Calf Serum), 2 mM L-glutamine (Sigma Aldrich, Chemie GmbH, München, Germany) and 1 % (v/v) penicillin/streptomycin (Biochrom AG, Berlin, Germany). 500 μl of a suspension of PBMCs (2 × 106 cells/ml) were incubated in sterile 24-well plates (Multiwell™, Falcon®, Becton Dickinson Labware, NJ, USA) for 4 h at 37 °C and 5 % CO2 with corn starch and the four different Holi colours (see above), respectively, each at 1.5 × 106 particles/ml. The utilised concentration of the Holi colours and corn starch arose from dose-effect experiments that we performed with ambient dust (data not shown). Cells treated with PBS only (7.5 % v/v) served as negative control. Cells treated with LPS (Lipopolysaccharide) (Enzo Life Sciences, NY, USA) at 100 ng/ml served as positive control. Samples were centrifuged for five minutes at 300 g and supernatants were transferred to fresh cell culture plates and frozen at −20 °C until further analysed.
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2

Preparation and Purification of Protein Phosphatases

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Hydroxylamine (50% wt/vol) was obtained from Sigma-Aldrich (Merck Group, Munich, Germany), the protein phosphatase from bacteriophage k (kPPase) from New England Biolabs (Hertfordshire, UK) and the TLRactivating ligands Pam3CSK4 and R848 (Resiquimod) from InvivoGen. LPS (lipopolysaccharide) was from Enzo Life Sciences (Lausen, Switzerland), recombinant mouse IL-18 from R&D Systems (Minneapolis, MN, USA), Halo-Link Resin from Promega (Fitchburg, WI, USA), Protein G-Sepharose from Expedeon (Cambridge, UK), reagents for cell culture from Gibco Thermo Fischer Scientific (Cambridge, MA, USA), Immobilon-P PVDF membranes from Merck-Millipore (Merck Group) and Brefeldin A (420601) from BioLegend (San Diego, CA, USA). Other solvents and reagents were obtained from Sigma-Aldrich (Merck Group) or VWR International (Radnor, PN, USA). The deubiquitylases USP2 and Otulin were expressed and purified as described [53] .
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3

Murine Bone Marrow-Derived Macrophage Isolation

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Bone marrow-derived macrophages were obtained from male and female C57BL/6 wildtype mice (5–7 months old), which were received from the animal facility of the University Hospital Frankfurt. The mice were euthanized and both legs together with the hip were extracted. Tibias, femurs and the hip were individually flushed with sterile PBS, the cell suspension was collected, centrifuged and the pellet resuspended in ACK buffer (Lonza) to remove erythrocytes. The obtained white pellet was resuspended in DMEM containing 20 ng/ml macrophage colony-stimulating factor (M-CSF) (Biotrend) and 4×106 cells per well were seeded on a 6 well plate. After 7 days of differentiation macrophages were activated overnight in DMEM containing 25 ng/ml interferon-γ (IFN-γ) (PeProtech) and 100 ng/ml lipopolysaccharide (LPS) (Enzo Life Science) for M1 cells; and 25 ng/ml interleukin-4 (PeProTech) for M2 cells. DMEM was supplemented with 10% fetal calf serum (Sigma-Aldrich) and 1% penicillin/streptomycin (Sigma-Aldrich).
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4

Antibody Reagents for Autophagy Research

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The AGS3 polyclonal antibody has been described previously and was kindly provided Dr. D. Ma (15 (link)). The commercial antibodies used as follows: LC3B antibody (L7543), β-actin-peroxidase antibody (A3854) [Sigma-Aldrich]; LAMP-1 (1D4B), LAMP-2 (H4B4), and CD-63/LAMP-3 (H5C6) antibodies [Developmental Studies Hybridoma Bank]; TGN-46 (ab16059) and LAMP-1 (ab25630) [Abcam]; cathepsin D (sc-6486) [Santa Cruz]; Akt (11E7), phospho-Akt (Ser473) (D9E), TSC2 (D93F12), phospho-TSC2 (Thr 1462) (5B12), 4E-BP1 (53H11), phospho-4E-BP1 (Thr37/46) (236B4), p70 S6 kinase (49D7), phospho-p70 S6 kinase (Thr389) (108D2) and GAPDH (14C10) [Cell Signaling]; and TFEB antibody (A303-672A) [Bethyl Laboratories]. The following reagents were used phorbol12-myristate 13-acetate (PMA) [Sigma-Aldrich]; bafilomycin A1 and glycogen synthase kinase 3 (GSK3) inhibitor VIII [Calbiochem]; G418 sulfate [Cellgro]; lipopolysaccharide (LPS) [Enzo Life Sciences]; Staphylococcus aureus (Wood strain without protein A) BioParticles, Escherichia coli (K-12 strain) BioParticles and DQ-Red BSA [Molecular Probes].
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5

Purified Flagellin and Loxoribine Treatment

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Purified recombinant flagellin from Salmonella Typhimurium (FLA-ST Ultrapure) and loxoribine were purchased from InvivoGen (San Diego, CA, USA). Lipopolysaccharide (LPS) was purchased from Enzo Life Sciences (Lörrach, Germany). LY294002 was obtained from Cell Signaling Technology (Danvers, MA, USA), while wortmannin and rapamycin were purchased from Sigma-Aldrich (St. Louis, MO, USA). Akt inhibitor IV was obtained from Calbiochem (San Diego, CA, USA). LY294002, wortmannin, and rapamycin were solved in dimethyl sulfoxide (DMSO; Sigma-Aldrich, St. Louis, MO, USA). In all experiments using the inhibitors, DMSO-containing DMEM medium complete (see below; DMSO dilution at 1:1000 vol/vol) served as negative control. Anti-mTLR5 neutralizing IgG antibody was obtained from InvivoGen.
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6

Neutrophil Isolation and Stimulation

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Neutrophils were isolated from peripheral blood using an EasySep direct human neutrophil isolation kit (Stemcell, Vancouver, BC). Cells were then counted and cultured at 107 cells/mL in RPMI supplemented with 5% fetal bovine serum and 1% penicillin/streptomycin. Neutrophil cultures were treated with GM-CSF (1–25 ng/mL, R&D Systems, Minneapolis, MN), FSTL1 (100–1000 ng/mL, R&D Systems), Interferon-γ (IFNγ) (10 ng/mL, R&D Systems), lipopolysaccharide (LPS) (1 μg/mL, Enzo Life Sciences, Farmingdale, NY), Interleukin 4 (IL-4) (20 ng/mL, R&D Systems), Interleukin 13 (IL-13) (20 ng/mL, R&D Systems), Interleukin 25 (IL-25) (10–100ng/mL, R&D Systems), Interleukin 33 (IL-33) (10–100 ng/mL, R&D Systems), thymic stromal lymphopoietin (TSLP) (10–100 ng/mL, R&D Systems) or Leukotriene C4 (LTC4) (10−6 –10−7 Cayman Chemical, Ann Arbor, MI) for 20 hours, cell culture supernatants were collected for protein analysis and cell lysates were collected to isolate RNA. Plates were coated with E-selectin, ICAM (50ng/well, Peprotech, Rocky Hill, NJ) or bovine serum albumin (BSA) (50ng/well, Sigma Aldrich) in pH 8 tris buffered saline (TBS) overnight at 4 degrees. Neutrophils were seeded into the wells and the culture supernatants were harvested at 20 hours.
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7

Murine Bone Marrow Macrophage Modulation

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BMMs were isolated from C57BL/6J mice as described above. Synthetic peptide Lv (DSLLAVRWFFAPDGSQEALMVKMTKLRIIQYYGNFSRTANQQRLRLLEE) was purchased from Phoenix Pharmaceuticals (Burlingame, CA, USA). Our pilot studies showed that while 1 μg/ml peptide Lv suppressed Tnfa expression, 0.1 μg/ml peptide Lv did not. Therefore, we used 1 μg/ml peptide Lv in this study.
BMMs were exposed to vehicle (α-MEM), 1 μg/ml lipopolysaccharide (LPS) (Enzo Life Sciences Inc., Farmingdale, NY, USA), or 1 μg/ml LPS + 1 μg/ml peptide Lv for 6 and 24 h. Thereafter, total RNA was extracted from BMM and used for cDNA synthesis based on a previously published protocol. The sequences of primers used for qRT-PCR are listed in Table 1. Relative Tnfa, Il1b, IL6, and Ifng expression was determined using CFX-96® (Bio-Rad, Richmond, CA, USA) and normalized to levels of the housekeeping gene, Gapdh. TNF-α and IFN-γ concentration in the supernatant 24 h after treatment was measured using a commercial ELISA kit (BioLegend) according to the manufacturer's protocol.
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8

Inflammatory Signaling Pathway Analysis

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The following reagents were purchased: docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA, Cayman Chemical); Poly(dA:dT), adenosine triphosphate (ATP), and nigericin (Sigma-Aldrich); Lipopolysaccharide (LPS, ENZO Life Sciences); purified flagellin (InvivoGen); neutralizing antibody to IL-1β (R&D Systems); caspase-1 antibody (Santa Cruz Biotechnology); NLRP3 antibody (ENZO Life Sciences); ASC antibody (Santa Cruz Biotechnology); and the appropriate secondary antibodies (Jackson ImmunoResearch Laboratory). For the ImageStream analysis a primary rabbit polyclonal NF-κB/p65 antibody (SantaCruz Biotechnology) was used with an Alexa647 conjugated donkey anti rabbit IgG antibody (Jackson ImmunoResearch Laboratories). DNA was stained using DAPI (20 µM).
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9

Isolation and Stimulation of Thioglycollate-Elicited Macrophages

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Four days after intraperitoneal injection of 2 mL of BBL thioglycollate medium [4% (wt/vol) brewer’s thioglycollate medium power (BD Biosciences)], thioglycollate-elicited macrophages were recovered in 5 mL of PBS by peritoneal lavage. Cells were seeded onto 96-well plates at 1 × 105 cells per well and cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (Gibco), 1% penicillin/streptomycin (Life Technologies) at 37 °C, and 5% CO2. Macrophages were stimulated for 4 h with Pam3CSK4 (40 ng/mL), poly(I:C) (20 μg/mL), lipopolysaccharide (LPS) (10 ng/mL), R848 (25 ng/mL) (all from Enzo Life Science), or CpG (Sigma-Aldrich, 100 μg/mL). dsDNA (IDT, 2 μg/mL) was complexed with Lipofectamine 2000 (Life Technologies) and transfected according to the manufacturer’s instructions. Nigericin (Sigma-Aldrich, 10 μg/mL) stimulation for 1 h was performed after 4-h LPS priming (10 ng/mL). Cytokine concentrations in the supernatants were measured using ELISA kits for mouse IFN-α, interleukin-1β, and TNF (eBioscience).
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10

SARS-CoV-2 RNA Fragment Synthesis

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Resiquimod (R848) and loxoribine were purchased from In vivoGen (San Diego, CA, USA). Lipopolysaccharide (LPS) was provided by Enzo Life Sciences (#ALX-581-012, Lörrach, Germany). TNF was acquired from Peprotech (#315-01A, Cranbury, NJ, USA). SARS-CoV-2 RNA fragments and control oligoribonucleotide, as indicated in the Figures and Table 1, were synthesized with 5′ phosphorylation and phosphorothioate bonds in every base (Integrated DNA Technologies, Coralville, IA, USA). Sequence information for all RNA fragments is provided in Table 1.
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