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10 protocols using imd0354

1

Caco-2 Cell Culture and Cytokine Treatment

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Caco-2 cells (A.T.C.C., Manassas, VA, U.S.A.) were cultured in DMEM (Dulbecco's modified Eagle's medium) supplemented with 10% (v/v) FBS (Gibco-BRL/Life Technologies), 1% NEEA (Gibco-BRL/Life Technologies) and 1% GlutaMAX™ (Invitrogen) at 37°C and 5% CO2. Cells were seeded in 24-well plates and, after attachment for 48 h, the medium was changed and the cells were incubated in the absence (controls) or presence of TNF-α (1–100 ng/ml, BioLegend) or the signalling pathway inhibitors celastrol (catalogue number 3203; Tocris) or IMD 0354 (catalogue number 2611; Tocris) 1 h before stimulation with TNF-α. Cell lysates were subjected to RNA isolation.
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2

Effects of PM2.5 Exposure on Cells

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Prior to treatment, the cells were plated at 2.5 × 105 cells/well in 6-well plates overnight. The next day, medium was removed, and the cells were incubated for another 24 h in serum-free DMEM. Medium was then removed again, and cells were treated with various concentrations of PM2.5 (0.01 – 30 μg/cm2) diluted in DMEM with 1% FBS, for the indicated times. In experiments where cells were treated more than once, medium was removed before each treatment, and cells were washed with PBS before being treated again with the respective concentration of PM2.5. Control cells in these repeated exposure experiments were also washed and had medium replaced with DMEM with 1% FBS alone. After the exposure period(s), cells were harvested for RNA or protein analysis. Prior to collection, photographic images of cells were taken with the Echo Revolution microscope for live-cell imaging. In some experiments, the cells were pre-incubated with the AhR antagonist CH223191 (10 μM, Tocris Bioscience, Ellisville, MO) or the NF-κB inhibitor IMD0354 (10 nM, Tocris Bioscience) for 30 min prior to addition of PM2.5. The concentrations of CH223191 and IMD0354 were chosen based on their effective inhibitory concentrations as reported in the literature (Tanaka et al., 2005 (link); Zhao et al., 2010 (link)).
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3

CRISPR-Cas9-Mediated REDD1 Knockout in Müller Cells

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Human MIO-M1 Müller cells were acquired from the UCL Institute of Ophthalmology (London, UK). REDD1 KO MIO-M1 cells were generated by CRISPR-Cas9 genome editing as previously described.36 MIO-M1 cultures were maintained in DMEM (Thermo Fisher Scientific, Waltham, MA, USA) containing 5.6 mM glucose and supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin. MIO-M1 cells stably expressing an shRNA targeting GSK3β were generated as previously described.29 (link),37 (link) Cells expressing pLKO.1-TRC were used as an shRNA control (Addgene Plasmid #10879). To model hyperglycemic conditions, culture medium was supplemented with d-glucose to achieve a final concentration of 30 mmol/L glucose for up to 24 h. Medium containing 5.6 mM glucose plus 24.4 mM mannitol was used as an osmotic control. Lipofectamine 2000 (Life Technologies, Carlsbad, CA, USA) was used for cell transfection. Plasmids included pCMV5 vector, pCMV-HA-caGSK3β, and pCMV-HA-REDD1.29 (link) In some studies, cell culture medium was supplemented with 1 µM IMD0354 (Tocris Biosciences, Bristol, UK) or 1 µM VP3.15 (MedKoo Biosciences, Durham, NC, USA).
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4

Evaluating NF-κB Modulators in Cell Assays

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NF-κB antagonist and agonists: TNFα (315–01A, Peprotech, Rocky Hill, NJ, USA ), Prostratin (5739, Tocris, Bristol, UK), CGS 21680 HCl (1063, Tocris), Betulinic acid (53603, Selleck Chemicals, Houston, TX, USA), PSI (4045, Tocris), Cardamonin (2509, Tocris), Bay 11–7082 (S2913, Selleck Chemicals), Bay 11–7085 (S7352, Selleck Chemicals), RO 106–9920 (1778, Tocris), TPCA-1 (S2824, Selleck Chemicals), Ikk-16 (S2882, Selleck Chemicals), PF 184 (4238, Tocris), IMD 0354 (2483, Tocris), Andrographolide (S2261, Selleck Chemicals), Costunolide (2483, Tocris), CID 2858522 (4246, Tocris), Pictilisib (S1065, Selleck Chemicals), Luteolin (S2320, Selleck Chemicals), Celastrol (1571, Tocris), Artemisinin (2668, Tocris). Cells were plated (at a seeding density of 1x104 for 96 well plates and 1x103 for 384 well plates) 12 h before treatment. Cells were treated with drugs at a range of concentrations either with fresh media (for agonists and vehicle only control) or fresh media with 5ng/ml TNFα (for antagonists and vehicle control) and incubated for 24 h. Each drug dose was performed in triplicate or quadruplicate and experiments were repeated at least three times.
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5

Evaluating IMD-0354 in Diabetic Rats

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IMD-0354 (Tocris 2611, Bristol, UK) was dissolved in 4% dimethyl sulfoxide (DMSO) (Sigma-Aldrich) immediately before the usage. Rats in the diabetic + IMD-0354 group were administrated IMD-0354 (30 mg/kg) intraperitoneally from week 6 of STZ injection for 6 consecutive weeks through the termination of the experiment. Rats in the control + IMD-0354 group were also given IMD-0354 (30 mg/kg) for six consecutive weeks, in order to assess the drug’s safety and potential side effects (1 (link)). Normal control and one group of diabetic rats received the same volume of 4% DMSO in phosphate-buffered saline (PBS; Gibco, Grand Island, NY, USA) at each time point. Under ketamine (80 mg/kg)- and xylazine (10 mg/kg)-induced anesthesia, the rats were killed by cervical dislocation, and then ocular samples were gathered for terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL), western blot, as well as immunofluorescence assessments.
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6

Gemcitabine and IL-1β Inhibition

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Gemcitabine was purchased from the Siteman Cancer Center Pharmacy. Details of inhibitors were: IRAK1/4 inhibitor (Sigma, cat# I5409), AS2444697 (Tocris, cat#5430), IMD-0354 (Tocris, cat#2611), anti-mouse IL-1β neutralizing antibody (Invivogen, clone 7E3), anti-human IL-1β neutralizing antibody (Invivogen, clone 4H5).
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7

Antimicrobial Compound Solubilization

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IMD0354 (Tocris 2611), gentamicin, daptomycin, and vancomycin (Sigma Aldrich) stocks were dissolved to 10 mg/mL in DMSO. Ciprofloxacin (Sigma Aldrich) was dissolved to 10 mg/mL in 0.1 N HCl.
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8

BAFF Protein Effects on B Cell Mitochondria

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Purified B cells (0.5 million/sample) were treated with 5 nM of BAFF 3-mer or 60-mer proteins in a complete culture medium in 96 well plates for 20 hours, the cells were stained with 200 nM MitoTracker Green FM (Fisher Scientific, M7514), 100 nM Tetramethylrhodamine, Ethyl Ester, Perchlorate (TMRE) (Fisher Scientific, T669), and 2.5 μM Invitrogen CellROX Green Reagent (Fisher Scientific, C10444) in RPMI 1640 media for 20 minutes at 37 °C. LPS (1 μg/ml) was used as a positive control for B cell activation and 20 μM BAM15 was used as a negative control for dissipation of mitochondrial membrane potential detected by TMRE. The cells were pre-treated for 1 hour with a vehicle (complete culture medium with 0.1 % Dimethyl sulfoxide or various inhibitors of NF-κB signaling in 0.1% Dimethyl sulfoxide: BMS-345541 (5 μM, #16667, Cayman Chemicals, US), BI 605906 (5 uM, #5300, Tocris, US), and IMD 0354 (1 uM, #2611, Tocris) before treating with BAFF proteins. After the staining, the samples were run on the Flow cytometer machine Becton Dickinson LSRFortessa (equipped with laser lines 355nm, 405nm, 488nm, and 640nm). Dead cells were discriminated by using DAPI. Data analysis and quantification were performed using FlowJo v10.6.2.
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9

In Vitro and In Vivo Anticancer Drug Screening

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All reagents and drugs were obtained from the following (Table S2): Gemcitabine and irinotecan (Washington University Siteman Cancer Center Pharmacy), 5-FU (Sigma-Aldrich #F6627), oxaliplatin (Sigma #O9512), SN-38 (Sellekchem #S4908), PF3644022 (Tocris #4279), (5Z)-7-Oxozeaenol (Tocris #3604), hydroxychloroquine (Sigma-Aldrich #H0915), recombinant TNFα (BioLegend #570104), trametinib (Selleckchem #S2673), AS2444697 (Tocris #5430), KU55933 (Selleckchem #S1092), VE821 (Selleckchem #S8007), SP600125 (Selleckchem #S1460), IMD0354 (Tocris #2611), GSK963 (Selleckchem cat# S8642). ATI-450 was provided by Aclaris Therapeutics Inc. under material transfer agreement. For in vivo experiments, ATI-450 was formulated in chow at 1000 parts per million, which achieved >60% inhibition of LPS-induced TNFα expression in mice (51 (link))
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10

Immunoblotting Assay for Cell Signaling

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Anti-p-NF-κB p65, anti-NF-κB p65, anti-p-c-Jun, anti-p-interferon regulatory factor 3 (p-IRF3), anti-IRF3, anti-p-IKKα/β, anti-GAPDH, anti-nuclear erythroid-related factor 2 (NRF2), anti-p53 tumor suppressor (p53), anti-p-JNK, and anti-JNK were purchased from Cell Signaling, Danvers, MA, USA; anti-c-Jun and anti-IKKα/β from Santa Cruz, Dallas, TX, USA; and anti-HSP70 from Abcam, Cambridge, UK. Horseradish peroxidase (HRP)-conjugated rabbit anti-goat IgG, HRP-conjugated goat anti-rabbit IgG, and HRP-conjugated goat anti-mouse IgG were purchased from ThermoFisher, Waltham, MA, USA. APAP, sulfasalazine, and NAC were purchased from Sigma-Aldrich, St. Louis, MO, USA; IMD-0354 from TOCRIS, Bristol, UK; rhHMGB1 from R&D Systems, Minneapolis, MN, USA; and rhHSP70 from ENZO, New York, NY, USA.
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