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1

Inflammatory Signaling Pathway Modulators

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LPS from Escherichia coli 0111:B4, oligomycin, carbonyl cyanide-p-trifluoromethoxyphenylhydrazone (FCCP), rotenone, mitomycin C, HMGB1, and BrdU were purchased from Sigma-Aldrich. The following kinase inhibitors were purchased from Tocris: leucine-rich repeat kinase 2-IN-1, BMS509744, GSK650394, and GSK2250665A. IRAK-1/4 inhibitor 1 was purchased from Sigma-Aldrich, SBI-0206965 and GNF-2 were obtained from Selleckchem, P-M2tide was obtained from Enzo Life Sciences, and MlkL inhibitor was obtained from Calbiochem. AZD7545 was kindly provided by Professor In-Kyu Lee at Kyungpook National University.
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2

Cellular Signaling Pathway Analysis

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Nilotinib was provided by Novartis, and GNF-2, GNF-5, and E64C were from Selleck. Antibodies were obtained commercially. R&D Systems: cathepsin L (AF952), human cathepsin B (AF953), mouse cathepsin B (AF965); Sigma Aldrich: β-actin, Arg (5C6; western blot), Flag (M2); Santa Cruz Biotechnology: Abl (K12; kinase assay), Abl (8E9; western), Ets1 (N-276), Sp1 (1C6), Sp3 (D-20), IKK-β (H-4), p65/RelA (C-20), and HRP-conjugated secondary antibodies. Cell Signaling: pCrk/CrkL (Y221/Y207), pRelA/p65 (93H1), IκBα (L35A5); BD Biosciences: Abl (8E9; western); Bioworlds: pEts1 (BS4316); ThermoFisher Scientific: β-tubulin; and Millipore: lamin A/C (clone 14), Sp1 (07–645). The Arg antibody used for kinase assays was previously described (49 (link)). ChIP antibodies were obtained from Active Motif: Sp1 (39058), Ets1 (39580), p65 (40916).
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Kinase Inhibitor Assay Protocol

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Imatinib, nilotinib, dasatinib, bafetinib, ponatinib, DCC-2036, GNF-2, GNF-5, EPZ005687, XAV-939, and FH535 were purchased from Selleckchem (Houston, TX, USA). PHA665752 was purchased from MedChemExpress, LLC (Princeton, NJ, USA). U0126, LY294002, and SP600125 were purchased form Wako (Tokyo, Japan). These reagents were dissolved in dimethyl sulfoxide and diluted in phosphate-buffed saline (PBS; 0.05 M, pH 7.4), filtrated through syringe filters (0.45 μm, IWAKI GLASS, Tokyo, Japan), and used for various assays described below.
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4

High-throughput Compound Screening in Cell Lines

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Roswell Park Memorial Institute (RPMI) 1640 medium, Dulbecco's modified Eagle's medium (DMEM), Dulbecco's phosphate-buffered saline (DPBS), trypsin, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), non-essential amino acids (NEAA), sodium pyruvate, blasticidin, penicillin/streptomycin, and CCF4 reagents were purchased from Life Technologies. Defined and dialyzed fetal bovine serum (FBS) was acquired from Thermo Fisher Scientific. ME-180 cell line, McCoy's 5A medium, and FBS were purchased from American Type Culture Collection (ATCC). Nano-Glo, CellTiter Blue, CellTiter Glo reagents were acquired from Promega. The NCATS Pharmaceutical Collection (NPC) library [8 ] was prepared as stock solutions in DMSO in 1536-well plates, where each plate corresponds to an indicated concentration of test compounds. G418 was purchased from Sigma-Aldrich. Azacitidine, AZD5363, bortezomib, camptothecin, enzastaurin, GDC-0994, GNF- 2, mitoxantrone, mycophenolate mofetil, niclosamide, OSI-906, PHT-427, PI-103, PP-242, selumetinib, TAK-632, trametinib, topotecan, volasertib, and YC-1 were purchased from SelleckChem. Cylcoheximide was purchased from Tocris Bioscience. The compound purity and identity were confirmed by quality control analysis at NCATS.
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5

Purification of Recombinant RANKL Protein

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The pGEX‐4T‐1‐rRANKL vector was a generous gift from Dr. Steven Teitelbaum that encodes the GST fusion construct containing the biologically active extracellular domain of RANKL (GST‐RANKL).30, 31 The plasmid was transformed into and expressed in Origami B(DE3) cells (EMD Millipore, Billerica, MA, USA) that co‐expresses chaperone proteins and was generously provided by Dr. Ding Xu. The GST‐RANKL fusion protein was purified using a BioScale Mini Profinity GST cartridge (Bio‐Rad, Hercules, CA, USA) and a subsequent size‐exclusion chromatography step. Endotoxins were removed using the Pierce High Capacity Endotoxin Removal Resin (Thermo Fisher Scientific, Waltham, MA, USA). GNF‐2 was obtained from Selleck Chemicals (Houston, TX, USA).
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