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24 protocols using fedratinib

1

Modulation of JAK/STAT3/FOXO3 Signaling

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The mouse macrophage cell line RAW264.7, the human colorectal adenocarcinoma cell line Caco-2, and the human normal colon epithelial cell line NCM460 were obtained from ATCC. All cells were maintained in DMEM medium (Gibco, USA) with 10% fetal bovine serum (Procell, China) in a humidified atmosphere containing 5% CO2 at 37 ℃. RAW264.7 cells were seeded in a 24-well culture plate at a density of 5.0 × 105 cells/mL and stimulated with 1 µg/mL lipopolysaccharide (LPS from Escherichia coli serotype 055:B5, Sigma‒Aldrich, USA) for 6 h to induce M1 macrophage polarization. To evaluate the effect of the STAT3 inhibitor S3I-201 (Abcam, UK) and the JAK2 inhibitor fedratinib (SAR302503, Selleck, China) on JAK/STAT3/FOXO3 signaling, cells were incubated with 7-mix (2− 2, namely 2.5 × 107 CFU), mix-sup (2− 4), S3I-201 (50 µM), fedratinib (10 µM), or S3I-201 + fedratinib for 4 h.
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2

Modulating Immune Responses with Targeted Inhibitors

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DNase I (HY‐P72974, MedChemExpress, Monmouth Junction, NJ, USA) was used to degrade NETs and NEi (GW‐311616; HY‐15891, MedChemExpress) was used to inhibit neutrophil elastase. Fedratinib (S2736, Selleck, Houston, TX, USA) was used to inhibit JAK2, C188‐9 (S8605, Selleck) was used to inhibit STAT3, and fisogatinib (BLU‐554; S8503, Selleck) and BLU9931 (A8706, APExBIO, Houston, USA) were used to inhibit FGFR4. Clodronate liposomes (40337ES10, YEASEN Biotechnology, Shanghai, China) was used for macrophage depletion, and diphtheria toxin (D0564, Sigma‐Aldrich, St. Louis, MO, USA) was used for dendritic cell depletion.
Recombinant human FGF19, IL‐1α, CXCL11, MIF and PAI‐1 were purchased from R&D Systems (Minneapolis, MN, USA). Recombinant human IL‐1β, IL‐18, and complement C5a were purchased from Novoprotein (Shanghai, China).
Human FGF19 neutralizing antibody (AF969, R&D Systems), human IL‐1β neutralizing antibody (AF‐201‐NA, R&D Systems), and human complement C5a neutralizing antibody (MAB2037, R&D Systems) were used in this study. Mouse Ly‐6G antibody (16‐5931‐85, eBioscience, San Diego, CA, USA) was used for neutrophil depletion, mouse asialo GM1 antibody (16‐6507‐39, eBioscience) was used for NK cell depletion, and mouse CD20 antibody (152104, Biolegend, San Diego, CA, USA) was used for B cell depletion.
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3

Synergistic effects of docetaxel and JAK inhibitors

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Docetaxel and JAK inhibitors (baricitinib, ruxolitinib and fedratinib) were purchased from Selleckchem, Houston, TX, USA. For drug combination studies, cells were seeded overnight in 96‐well plates at a density of 5000 cells/well. Cells were treated with docetaxel and/or JAK inhibitors (baricitinib, ruxolitinib and fedratinib) alone or in combinations at dose‐response matrix format. Plates were then incubated at 37°C in a humidified 5% CO2 incubator for 72 hours. The plates were terminated by MTT cell proliferation assay at 72 hours after treatment. Calcusyn 2.1 software (Biosoft, Cambridge, UK) was used to generate combination index (CI) based on Chou‐Talalay method, in which CI <1, = 1 and >1 indicates synergism, additive and antagonism effect, respectively (Table S1).21 (link), 22 (link), 23 (link), 24 (link), 25 (link) The dose‐response surface curves with levels of highest single agent (HSA) synergy were plotted by Combenefit software (Cancer Research UK Cambridge Institute).21 (link), 22 (link), 26 (link)
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4

Mass Spectrometry Analysis of Screened Compounds

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D-luciferin was purchased from Gold Biotechnologies (St. Louis, MO). Screened compounds are described below. Repurchased hits, including Momelotinib, TG101209, Fedratinib, Pacritinib, Danusertib, Saracatinib, Ibrutinib, and Bosutinib were obtained from Selleck (Houston, TX). For mass spectrometric experiments, LC–MS grade acetonitrile (ACN) and water were from J.T. Baker (Philipsburg, NJ). Formic acid was obtained from Pierce (Rockford, IL) and iodoacetamide (IAA) and dithiothreitol (DTT) were purchased from Sigma-Aldrich (St. Louis, MO). Sequencing grade trypsin was supplied by Promega (Madison, WI).
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5

Radiolabeled Compounds for Cellular Assays

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All radiolabeled chemicals were purchased from American Radiolabeled Chemicals Incorporation (St. Louis, MO, USA), PerkinElmer (Boston, MA, USA), or Moravek Biochemicals (Brea, CA). The specific activity of each radiolabeled chemical was as follows: metformin (1,1-dimethylbiguanide [biguanido-14C] hydrochloride) (110.2 mCi/mmol), thiamine [3H(G)] hydrochloride (20 Ci/mmol), carnitine hydrochloride, l-[N-methyl-3H] (80 Ci/mmol), histamine (2-(4-imidazoyl)ethylamine dihydrochloride [3H]) (14.2 mCi/mmol), [3H] norepinephrine (44.7 mCi/mmol), [3H] serotonin (hydroxytryptamine, 5-[1,2-3H] creatinine sulfate) (20.3 mCi/mmol), [14C] TEA (tetraethylammonium) (50 mCi/mmol), [3H] MPP+ (1-methyl-4-phenylpyridinium) (85.5 mCi/mmol), choline chloride [1,2-14C] (50 mCi/mmol), [14C]-guanidine HCl (53 mCi/mmol), famotidine [3H(G)] (20 Ci/mmol), and [14C]-aminoguanidine (57.7 mCi/mmol). Unlabeled chemicals were purchased from Sigma (USA). Fedratinib was purchased from Selleck Chemicals (Houston, TX). Cell culture supplies were purchased from the Cell Culture Facility (UCSF, California, USA).
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6

Venetoclax and Fedratinib Combination Assay

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Venetoclax (1 mL*10 mM in DMSO) and powdered compound were purchased from TargetMol. Fedratinib (1 mL*10 mM in DMSO) was purchased from Selleckchem and powdered was purchased from MedChemExpress. All concentrations for in vitro studies were made at 2x or 4x for combination studies and diluted in RPMI-10 for plating assays. Cells were treated with a range of doses ranging from 1nM to 10uM.
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7

Culture and Maintenance of MDS Cell Lines

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Human MDS92 and MDS-L cells (22 (link), 23 (link)) were a gift from D. T. Starczynowski, University of Cincinnati (25 (link)). MDS92 and MDS-L cells were cultured in RPMI 1640 (Thermo Fisher Scientific, Waltham, MA) with 10% fetal bovine serum (MilliporeSigma, Burlington, MA) and IL-3 (10 ng/ml; PeproTech). OCI-AML3, DAMI, TF-1 Kasumi-1, and KG-1 cells were purchased from the American Type Culture Collection and cultured under previously described conditions (46 (link)–48 (link)). All the cell lines were cultured with 2 mM l-glutamine, penicillin (100 U/ml), and streptomycin (100 μg/ml) at 37°C in 5% CO2. Primary CD34+ cells were cultured as previously described (49 (link)). Chlophosome-A chlodronate liposomes were purchased from FormuMax Scientific (#F70101C-A). Fedratinib was purchased from Selleckchem (TG101348) and was diluted in dimethyl sulfoxide.
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8

Immunoprecipitation and Western Blot Analysis

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The following reagents and antibodies were purchased from commercial sources: inhibitor cocktail (Trichostatin A (TSA, T8552, Sigma), protease inhibitor cocktail (P8340, Sigma), phosphatase inhibitor cocktail (P0044, Sigma)), fedratinib (S2736, Selleckchem), universal nuclease (88700, Thermo Fisher), Bradford assay (23200, Thermo Fisher), dithiothreitol (DTT; DTT100, Goldbio), enzyme-linked chemiluminescence (ECL) plus (32132, Thermo Fisher), SYBR Green PCR Master Mix (4472908, Applied Biosystems), streptavidin agarose (20359, Thermo Fisher), Protein A/G PLUS-Agarose (sc-2003, Santa Cruz Biotechnology), anti-Flag agarose gel (A2220, Sigma) and anti-HA affinity gel (E6779, Sigma). Antibodies were as follows: STAT3 (9139, CST), phospho-STAT3 (Tyr705) (ab76315, Abcam), β-actin (C4) HRP (SC-47778, Santa Cruz), Na/K-ATPase (SC-21712, Santa Cruz), histone H3 (4499S, CST), Flag HRP (A8592, Millipore), HA-probe (Y-11) (SC805, Santa Cruz), HA-probe (F-7) (SC7392, Santa Cruz), DHHC7 (ab138210, Abcam), DHHC7 (R12–3691, Assay Biotechnology), Alexa Fluor 350 goat anti-rabbit IgG (A-11046, Invitrogen), Alexa Fluor 594 goat anti-mouse IgG (8890S, CST), mouse CD4 PerCP-Cy5.5 (560767, BD Pharmingen), mouse IL-17A PE (560767, BD Pharmingen), anti-mouse IgG HRP (7076S, CST) and anti-rabbit IgG HRP (7074S, CST).
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9

Immunoblotting Analysis of Phospho-Proteins

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Antibodies against phospho-AKT(Ser473), ERK, phospho-ERK(Thr202/Tyr204), STAT5, and phospho-STAT5 were obtained from Cell Signaling Technology (Danvers, MA); anti-KIT from R&D Systems (Minneapolis, MN) and Santa Cruz Biotechnology (Santa Cruz, CA); anti-phospho-KIT(Tyr823) from Invitrogen (Carlsbad, CA); anti-AKT from BD Biosciences (San Diego, CA); and anti-β actin from Sigma Aldrich (St. Louis, MO); and anti-rabbit IgG 800CW and anti-mouse IgG 680 RD from Licor Biosciences (Lincoln, NE). Human TruStain FcX and APC-conjugated anti-human c-KIT (clone 104D2), unlabeled anti-human KIT antibody (clone 104D2) and Zombie Aqua fixable viability dye were obtained from Biolegend (San Diego, CA); KIT antibody for IHC from Dako-Agilent (Santa Clara, CA); human SCF from R & D Systems; avapritinib, imatinib, dasatinib, midostaurin, fedratinib, STAT5-IN-1, SH4-54, venetoclax, ripretinib (DCC-2618), ruxolitinib, tofacitinib, and C188-9 from SelleckChem (Houston, TX); LY294002 and U0126 from Tocris (Minneapolis, MN); Pierce BCA assay and CyQuant cell proliferation assay from Thermo Fisher Scientific (Waltham, MA); and ViaStain propidium iodide (PI) staining solution from Nexelom Biosciences (Lawrence, MA).
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10

Biotechnology Acquisitions for Research

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UA was purchased from Pureone Biotechnology, (Shanghai, China). Fedratinib and cryptotanshinone were purchased from Selleck Chemicals (Shanghai, China).
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