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38 protocols using nutlin 3

1

Flow Cytometry and Western Blot Analysis of Cell Signaling Pathways

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The following antibodies were used in flow cytometry: phycoerythrin (PE)-conjugated anti-mouse CD44 (Biolegend, 103007), Sca-I (eBioscience, 12-5981-83), CD140a (Biolegend, 135906), CD13 (BD Pharmingen, 558745), MHC II (eBioscience, 12-5320-80), CD11b (eBioscience,12-0112-83), CD11c (eBioscience, 12-0114-82), CD86 (eBioscience, 12-0862-82), and CD45 (eBioscience, 12-0451-82). Antibodies used for western blotting analysis were: anti-p53 (FL-393; sc-6243, Santa Cruz Biotechnology); GAPDH (14C10, 2118, Cell Signaling Technology). Antibody used for Chip was: p53 (FL-393; sc-6243, Santa Cruz Biotechnology), IgG (normal mouse IgG, sc2025, Santa Cruz Biotechnology). The reagents for cell treatment were: Nutlin-3 (Nutlin-3, Selleck Chemicals, Houston, TX, USA), Cisplatin (Sigma-Aldrich), RANKL (recombinant mouse RANKL, 50 ng/ml, R&D), M-CSF (recombinant mouse M-CSF, 25 ng/ml, R&D), and OPG (recombinant OPG, 50 ng/ml, Sigma-Aldrich). RANKL for mouse injection (recombinant mouse RANKL, 2 mg/kg/day) was from R&D Systems.
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2

Western Blot Analysis of Cellular Proteins

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The antibodies included the following: anti-SQSTM1/p62 (M162-3, Medical Biological Laboratories, Japan), anti-SQSTM1/p62 (ab109012, Abcam, USA), anti-p53 (sc-126, Santa Cruze Biotechnology, USA), anti-p53 (10,442–1-AP, Proteintech, China), anti-mutant p53 (ab32049, Abcam), anti-NRF2 (M200-3, Medical Biological Laboratories), anti-NRF2 (16,396–1-AP, Proteintech), anti-ubiquitin (10,201–2-AP, Proteintech), anti-GAPDH (#5174, Cell Signaling Technology), anti-β-actin (#4970, Cell Signaling Technology), anti-HA (M180-3 and M561, Medical Biological Laboratories), anti-His (D291-3, Medical Biological Laboratories), anti-Flag (M185, Medical Biological Laboratories), anti-Flag (20,543–1-AP, Proteintech), anti-SLC7A11 (NB300-318, Novus, USA), anti-SLC7A11 (26,864–1-AP, Proteintech) anti-HO1 (ab68477, Abcam), anti-HO1 (10,701–1-AP, Proteintech), anti-NQO1 (ab80588, Abcam), anti-Keap1 (10,503–2-AP, Proteintech).
The reagents included the following: Erastin (S7242, Selleck, USA), APR-246 (HY-19980, MCE, USA), Pifithrin-α (HY-15484, MCE), Nutlin-3 (S1061, Selleck).
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3

Investigating Mechanisms of Cell Cycle Regulation

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Cells were treated with 5 nM ActDL (Sigma-Aldrich, A1410) or 2 μM BMH-21 (Sigma-Aldrich, SML1183) for 24 hours. CHX (Sigma-Aldrich, C4859) was used at a working concentration of 100 μg/ml for 30 min or the indicated time points. For DOX induction (Sigma-Aldrich, D9891), cells were treated with DOX (1 μg/ml; Sigma-Aldrich, D9881) for 48 to 72 hours, unless otherwise indicated. Pan-caspase inhibitor Z-VAD-FMK (R&D Systems, FMK001) and caspase 2 inhibitor Z-VDVAD-FMK (R&D Systems, FMK003) were used at a final concentration of 20 μM for 1 hour or the indicated time points. MG132 (Sigma-Aldrich, M7449), Nutlin-3 (Selleckchem, S1061), and MLN4924 (Selleckchem, S7109) were added to cells in a final concentration of 10, 5, and 1 μM, respectively, for 24 hours. Camptothecin (Sigma-Aldrich, C9911) was used at a working concentration of 5 μM and 5-fluorouracil (Sigma-Aldrich, F6627) at 10 μg/ml. Neocarzinostatin was used at 0.5 μg/ml for 24 hours, LMB was used at 20 ng/ml for 6 hours, and pladB was used at 1 μM for 6 hours. For chemical inhibition of eIF4A3, 52a, or 52b, 53a from (31 (link)) was used at 5 μM for 24 hours. For cell synchronization at G2, cells were treated with nocodazole (Sigma-Aldrich, M1404) at 400 nM for 16 hours.
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4

Cloning and Characterization of Human p53

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The human p53 gene containing a His-tag was amplified from the genome of HEK293 cells and then cloned into the pCDNA3.1(+) vector (Invitrogen, Waltham, USA) with the BamHI and XhoI restriction enzymes (Thermo Scientific, Waltham, USA). The interferon stimulated response element (ISRE) / luciferase (pISRE-Luc) reporter plasmid was kept in our laboratory. The internal control plasmid encoding Renilla luciferase (phRL-TK) and the Dual-Luciferase Reporter Assay System were purchased from Promega Corporation (Madison, USA). The p53 activator Nutlin-3 was purchased from Selleck (Houston, USA). Antibodies against p53 (1C12) and the His-tag (27E8) were purchased from Cell Signaling Technology (Danvers, USA). Antibody against β-actin (AC-74) was purchased from Sigma–Aldrich Corporation (St. Louis, USA). Mouse anti-PEDV spike protein (PEDV-S) monoclonal antibody (3F12) was purchased from Median Diagnostics Inc (Chuncheon, South Korea). Mouse polyclonal antibody against PEDV nucleocapsid protein (PEDV-N) was prepared by our team in our previous study (Shi et al., 2014 ). The human IFN-beta ELISA Kit was purchased from R&D (Minneapolis, USA).
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5

Evaluation of Bioactive Compounds in Cell Screening

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Camptothecin (Cat# S1288), vinblastine (Cat# S1248), pimasertib (Cat# S1457), trametinib (Cat# S2673), ABT-737 (Cat# S1002), A-1155463 (Cat# S7800), and nutlin-3 (Cat# S1061) were purchased from Selleck Chemicals (Houston, TX). Bortezomib (Cat# NC0587961), etoposide (Cat# ICN19391825), MG-132 (Cat# 17-485), and Q-VD-OPh (Cat# OPH00101M) were purchased from Thermo Fisher Scientific. N-acetylcysteine (Cat# A8199), thapsigargin (Cat# T9033), tunicamycin (Cat# T7765), paclitaxel (Cat# T7191), JNK Inhibitor VIII (Cat# 420135), 2-deoxyglucose (Cat# D8375), oligomycin (Cat# O4876), and cycloheximide (Cat# C7698) were obtained from Sigma-Aldrich (St. Louis, MO). S63845 (Cat#21131) was obtained from Cayman Chemical (Ann Arbor, MI). Staurosporine (Cat# A8192) was obtained from ApexBio (Houston, TX). Erastin was the kind gift of Brent Stockwell (Columbia University). Erastin2 (compound 35MEW28 in Dixon et al., [2014 (link)]) and ML162 (CAS: 1035072-16-2) were synthesized by Acme Bioscience (Palo Alto, CA). Chemical screening was conducted as described below; the library of 261 bioactive compounds was obtained from Selleck Chemicals (Cat# L2000).
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6

Evaluating Anti-Cancer Drug Synergies

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Rapamycin was from the NCI drug repository. AZD8055, MK2206, PD0332991 and Nutlin 3 were from Selleck Chemicals (Houston, TX). The detailed information of these drugs is listed in Supplementary Table 1.
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7

Evaluation of Anti-Cancer Compounds

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Tozasertib, alisertib, and nutlin-3 were purchased from Selleck Chemicals (Houston, Tx, USA), cisplatin and vincristine from Gry-Pharma GmbH (Kirchzarten, Germany), and doxorubicin from Cell-Pharm GmbH (Bad Vilbel, Germany).
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8

Anticancer Small Molecule Protocol

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The following small molecule compounds targeting the RTK/Ras/PI3K pathway were diluted in DMSO (Sigma-Aldrich, St. Louis, USA): lapatinib ditosylate was obtained from Santa Cruz Biotechnology (Dallas, USA) (catalog number 202205A). Crizotinib (S1068), NVP-BKM120 (S2247), GDC-0068 (S2808), AZD2014 (S2783), AZD8055 (S1555) and GSK2636771 (S8002) were obtained from Selleck Chemicals (Houston, USA).
The following small molecule compounds targeting the Rb pathway were diluted in DMSO: SNS-032 (S1145) was obtained from Selleck Chemicals. Palbociclib isethionate (PD-0332991) (S1579) was diluted in milliQ water and was obtained from Selleck Chemicals.
The following small molecule compounds targeting the p53 pathway were diluted in DMSO: Nutlin3 (S1061) and Alisertib (MLN8237) (S1133) were obtained from Selleck Chemicals. PRIMA-1MET (SC-361295) was obtained from Santa Cruz Biotechnology.
The following small molecule compound was identified as a potential combination partner of AZD8055 and was diluted in DMSO: ABT-263 (11500) was obtained from Cayman Chemical (Ann Arbor, USA).
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9

Evaluation of Small Molecule Inhibitors

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Palbociclib (PD-0332991)(#S1116), Imatinib (STI571)(#S2475), Nutlin-3 (#S1061), and NVP-BGJ398 (#S2183), were all purchased from Selleck Chemicals (Munich, Germany) and dissolved in DMSO (Sigma-Aldrich, Missouri, USA) according to the manufacturers recommendation.
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10

Culturing Human Liver and Kidney Cell Lines

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The human hepatoma cell lines HepG2, Hep3B and the human embryonic kidney cell line HEK293T were purchased from ATCC cell bank in 2014. The human hepatoma cell line Huh7 was purchased from the cell bank of the Shanghai Institute of Cell Biology (Shanghai, China) in 2017. HepG2 and Hep3B were maintained in Minimum Essential Medium (MEM, Gibco, Thermo, USA). Huh7 and 293T were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, Thermo, USA). The complete cell culture mediums were supplied with 10% fetal bovine serum (FBS, Excel, Australia), 100 U/ml penicillin and 100 μg/ml streptomycin. Cells were incubated in a CO2 incubator at 37 °C, with 5% CO2. All the cell lines were used for less than 25 passages from acquisition to discard. Pifithrin-α (PFT-α) was purchased from Santa Cruz Biotechnology (USA), nutlin-3 was from Selleck Chemicals (USA) and TPEN was from Sigma-Aldrich Inc. (USA). For the inhibitory assay, PFT-a (20 μM), nutlin-3 (50 nM) and TPEN (100 nM) were dissolved in DMSO, Milli-Q sterile water or ethanol, respectively, and applied to pretreat the cells.
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