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23 protocols using lipopolysaccharides (lps)

1

Generation of NF-κB Luciferase-Expressing Alveolar Cell Line

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A spontaneously transformed type II mouse lung alveolar epithelial cell line [19] (link) (C10) was cultured as described previously [20] (link). A C10 cell line stably expressing NF-κB luciferase was generated as previously described [21] (link). Briefly, C10 cells were transfected with the plasmid, 6 κB-tk-luc, in the presence of the plasmid PSV-2Neo (Promega), conferring a resistance to neomycin. Following incubation with the antibiotic, geneticin, antibiotic-resistant colonies were propagated. C10 cells were starved in medium containing 0.5% FBS for 16 h prior to exposure of 1 µg/mL LPS (List Biological Laboratories, Inc).
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2

Silica-induced IL-1β Secretion in BMDMs

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BMDMs (1×105/well) were seeded into 48-well plates and cultured overnight. Then cells were primed with 10 ng/mL lipopolysaccharide (LPS; List Biological Laboratories, Campbell, CA). Five hours later, cells were stimulated with the indicated dose and size of silica particles or with 1 mM ATP (Wako, Osaka, Japan) for four hours at 37°C. For some experiments, LPS-primed BMDMs were pretreated with 20 μM of cytochalasin D (Cyto D; Wako, Japan), or 200 nM of Bafilomycin A1 (Sigma-Aldrich, St Louis, MO) for 1 hour, and were then stimulated with silica particles for 4 hours. The amount of IL-1β in cell culture supernatants was measured by an enzyme-linked immunosorbent assay (ELISA) kit (eBioscience, San Diego, CA) according to the manufacturer’s instructions.
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3

Synovial Fibroblast Stimulation Assay

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Synovial tissues were obtained from patients with RA diagnosed according to the 1987 American College of Rheumatology criteria for classification of RA,[19 (link)] who underwent joint reconstruction surgery (n = 32). Synovial tissues from patients with osteoarthritis (OA, degenerative disease) served as controls (n = 27). The study was approved by the Kantonale Ethikkommission der Kanton Zurich, with the approval numbers 475 and 515. All patients provided a written informed consent and the study was approved by the local Ethics committee. SF cultures were established by dispase digestion of synovial tissue as described elsewhere.[20 ] Cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum. SF of passages 4–8 were used for all experiments. RASF and OASF were stimulated or not for 24 hours with Poly(I:C) (10ug/ml; Invivogen), LPS (100ng/ml; List Biological Laboratories) or TNFα (10 or 100ng/ml; R&D) alone or in combination with IL1β (1ng/ml; R&D).
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4

Evaluating PHA 568487 Immunomodulatory Effects

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To evaluate the possible immunomodulatory effects of PHA 568487 in vivo, the air pouch model of acute inflammation was used [12 (link),25 (link)]. At 8 weeks of age, male C57BL/6JRj mice (Janvier Labs, Le Genest-Saint-Isle, France) were injected with 3 mL of sterile air between the scapulae under isoflurane anesthesia. Three days later, the air pouch was re-filled with 3 mL of sterile air. On the sixth day, the mice received an intraperitoneal injection of either PBS (Thermo Fisher Scientific, Waltham, MA, USA) or PHA 568487 (Tocris Bioscience, Ellisville, MO, USA) at 12.4 μmol kg−1 (5 mg/kg) or 123.4 μmol kg−1 (50 mg/kg). Fifteen minutes later, all mice were injected with LPS (10 μg, List Biological Laboratories Inc., Campbell, CA, USA) directly into the pouch. The mice were sacrificed six hours after the LPS injection by an overdose of pentobarbital (Apoteket AB, Stockholm, Sweden). Finally, the pouch cavity was flushed with 2 mL of PBS with 1.6 mmol L−1 of EDTA, and the exudate was collected. The white blood cell count of the exudate was analyzed using the Vetscan HM5 Hematology Analyzer (Abaxis, Union City, CA, USA) and thereafter centrifuged for 5 min at 400× g. Supernatants were stored at −80 °C until multiplex analysis.
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5

Macrophage Infection and Cytokine Response

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J774.16 macrophages were cultured in 24-well plates as previously described (VanderVen et al. 2015 (link)). Cells were seeded at 105 cells per well and were allowed to adhere overnight at 37°C and 5% CO2 prior to infection. The macrophages were infected with M. tuberculosis CDC1551 as previously described (VanderVen et al. 2015 (link)) at the indicated MOI. Following 2 h of infection, the cultures were washed twice with warm supplemented DMEM, replenished with the same medium containing 8Br-cAMP (Sigma) at the indicated concentrations, LPS 10 ng/ml (List Biological Laboratories), V-58 at the indicated concentrations, or DMSO vehicle control. At 18 h post-infection the culture supernatants were collected and used to quantify TNF-α levels by ELISA (eBioscience) following the manufacturer's instructions. Addition of 0.1 % DMSO was shown not to affect TNF-α levels (Figure S7).
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6

Postnatal Neuroinflammation in Mice

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All animals were kept on a 12 h dark-light cycle and standard housing conditions with ad libitum food access. On postnatal day 5 (P5), C57Bl/6J mice were randomly assigned to 4 experimental groups: LPS (1 mg/kg, #423, List Biological Laboratories, Campbell, CA, USA)-injected mice (n = 12, ♂ = 6, ♀ = 6) and saline (1 mg/kg, Sigma Aldrich, St. Louis, MO, USA)-injected mice (n = 12, ♂ = 6, ♀ = 6). Injections were performed intraperitoneally. This age in mice represents a critical brain developmental stage equivalent to preterm human infants [14 (link)]. Morphological analysis was performed 7 days after injection (P12). The P12 time point was studied as it corresponds to a stage in mouse brain development with high rate of brain growth, including gliogenesis, increasing axonal and dendritic density, and with significant brain plasticity activity [14 (link)]. Animals were anesthetized deeply with an intraperitoneal injection of pentobarbital (20 μL per animal, 60 mg/mL), followed by transcardial perfusion with histofix (Histolab products AB, Vastra Frölunda, Sweden) and collection of brains. One brain hemisphere (left or right) was randomly selected for each animal to have equal number of each hemisphere per group, immersed in the same fixative solution, and stored at 4°C for further brain structural quantification.
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7

Isolation and Culture of Bone Marrow-Derived Dendritic Cells

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C. neoformans-derived (C. neoformans-) MPs were isolated and purified as previously described (34 (link)).
Erythrocyte-depleted bone marrow cells from flushed marrow cavities of femurs and tibias of naïve wild type (IL-10+/+) or IL-10 deficient (IL-10−/−) mice were cultured in 10% CM supplemented with 20 ng/ml granulocyte macrophage colony-stimulating factor (GM-CSF; Pepro Tech, Inc., Rocky Hill, NJ) at a concentration of 1×106 cells/ml at 37ºC and 5% CO2 for 7 days. The culture was replenished with cytokine on day 3. At the end of culture, BM-DCs were harvested, enriched using 14.5% metrizamide (Nyegaard & Co., Oslo, Norway)-CM gradients and washed twice with PBS. BM-DCs [1×106 cells/ml of 10% CM with GM-CSF (20 ng/ml)] were then cultured in the presence of either C. neoformans-MPs (50 µg/ml), LPS (1 μg/ml; List Biological Laboratories, Campbell, California), or vehicle (PBS) at 37ºC and 5% CO2 for 24 hours. In some experiments, either a blocking anti-IL-10 receptor antibody (clone 1B1.3a, BioLegend, San Diego, CA, 20 µg/ml), an isotype-matched control antibody (rat IgG1k, clone RTK207, BioLegend), or recombinant mouse IL-10 (ThermoFisher Scientific, Rockford, IL, 3 ng/ml) were added to C. neoformans-MPs-pulsed BM-DC cultures.
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8

U937 Macrophage Polarization Protocol

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U937 cells were seeded in TomoDishes at about 5*104  cells per dish with complete media and PMA (Sigma-Aldrich 79346, 1  μM ). The complete media consisted of RPMI-1640 (Gibco, 11875-093), 10% heat-inactivated FBS (Corning, 35-010-CV), 1% P/S, 1%L-Glu (Gibco, 200 mM, 25030081), and 1% HEPES (Gibco, 1M, 15630-080). The seeding day is counted as day 0.
For M1 polarized cells, on day 3, PMA media is removed, and cells are washed with PBS. Thereafter, polarizing media consisting of complete media with LPS (List Biological Laboratories, 421, 100  ng/mL ) and IFN-y (Sigma-Aldrich, SRP3093, 50  ng/mL ) were added to the dish. The cells were incubated for another 2 days. On day 5, the media was removed, and cells were washed with PBS before fixing.
For M2 polarized cells, on day 3, PMA media is removed, and cells are washed with PBS. Thereafter, polarizing media consisting of complete media with IL-4 (Sigma-Aldrich, SRP3093, 50  ng/mL ) and IL-13 (R&D Systems, 213-ILB-005, 50  ng/mL ) were added to the dish. The cells were incubated for another 2 days. On day 5, the media was removed, and cells were washed with PBS before fixing.
The cells were fixed with 4% PFA at room temperature for 15 min. It was then washed with PBS two times. PBS was once again added to fully submerge the fixed cells before imaging.
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9

RAGE Knockdown Modulates TNF-α and LPS Responses

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HUVEC-L (Lonza) were grown to 90% confluence. RAGE gene knockdown was performed using adenoviral vector AGER shRNA or scramble shRNA control (200MOI, Vector Biolabs). Cells were transferred to 96 well plates at a density of 10 000 cells/well 48 h following shRNA treatments. Seventy-two hours following adenoviral treatment, cells were pretreated with 50uM Z-VAD-FMK (BD Biosciences) for 1 h prior to stimulation with 100 ng/ml recombinant human TNFa (Peprotech), 10ng/mL LPS (List Biological Laboratories, Campbell, CA, USA), or 10 μg/ml 2006 CpG-DNA (synthesized by Invivogen). Cells were incubated for 4 h at 37°C. Cell viability was quantified using CellTiter-Glo luminescent assay (Pro-mega). Luminescence was read on the Tecan Spark 10M luminometer.
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10

Infection and Stimulation of MDDCs

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MDDCs were infected or stimulated with innate agonists between day 4 and day 6 after differentiation. For infections with HIV-1 and related lentiviruses, except where noted otherwise, Vpx+ virus-like particles were used to overcome virus restriction (1 mL supernatant for 1 × 10^7 cells) (Johnson et al., 2018 (link); Manel et al., 2010 (link)). MDDCs were counted on day 4 and resuspended at 800,000 cell per ml in fresh medium with GM-CSF, IL-4, and polybrene (1 μg/ml) and then reseeded into appropriate culture vessels. For most assays, MDDCs were infected at a density of 800,000 cells per ml by diluting virus in MDDC media (without cytokines or polybrene) to a final volume normalized to controls. Innate and inflammatory stimuli were used at the indicated concentrations: poly(I:C) (InvivoGen, 10 μg/ml); LPS (List Biological Laboratories, INC, 1 ng/ml).
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