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9 protocols using marizomib

1

Characterization and Drug Response of R-HL60 Cells

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R-HL60 cells were established from parental HL60 cells (ATCC, Rockville, MD, USA) and were characterized as described previously [1 (link)]. HL60 and R-HL60 cells were cultured in RPMI 1640 medium (Cytiva, Marlborough, MA, USA) supplemented with 10% fetal bovine serum (Gibco, Amarillo, TX, USA) and 1% antibiotic-antimycotic reagents (Gibco). Cells were cultured at an incubator with 5% CO2 at a temperature of 37 °C, and the culture medium was changed every 2–3 days. Cytarabine, bortezomib, carfilzomib, and marizomib were purchased from Sigma Aldrich (St. Louis, MO, USA). R-HL60 cells were exposed to different concentrations of Cytarabine, bortezomib, carfilzomib, and marizomib, and the cell viability was measured using the CCK-8 assay (Sigma Aldrich, St. Louis, MO, USA) All data were compared with the vehicle control (ddH2O for Cytarabine treatment; dimethyl sulfoxide [DMSO] for bortezomib, carfilzomib, and marizomib treatment).
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2

Marizomib Cytotoxicity Assay

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Cells were seeded onto white 96-well plates and incubated for 16 h. Marizomib (SML1916, Sigma-Aldrich) was added at different concentrations in 6 technical replicates. After 72 h, cell viability was measured using the CellTiter-Glo reagent (Promega) according to the manufacturer’s instructions. Luminescence was measured using an automated plate reader (GloMax Discover microplate reader). Dose–response curves and half-maximal inhibitory concentration (IC50) values were calculated with GraphPad Prism software v8.4.3.
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3

Proteasome Activity Assay in Piglet Brain

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We measured proteasome activity using the Proteasome Activity Fluorometric Assay Kit I (UBPBio, Aurora, CO) per the manufacturer's instructions. First, we verified that the assay detects piglet proteasome activity using brain homogenate with and without the proteasome inhibitor, marizomib, 5 mmol/L (Sigma‐Aldrich). Then, we tested subcortical white matter and sensorimotor cortex in naïve piglets and those that received HI+hypothermia for 20 hours and HI+hypothermia for 29 hours. We selected these groups because neonates treated for moderate or severe HIE receive more than 29 hours of hypothermia in clinical practice. Bovine P20S was used as a positive control, and wells loaded with only cell lysis buffer were negative controls. Reactions were run in 0.2 μg of cell extract protein. Data are presented as enzyme activity.
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4

Cytotoxic Drugs Screening Assay

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The following drugs were used: camptothecin (CPT), actinomycin D, cycloheximide, marizomib, chloroquine, Bmh21, BO-2, (all Sigma-Aldrich), aphidicolin (Santa Cruz), talazoparib (Axon Medchem), quarfloxin (CX-3543, Adooq Bioscience) and CX-5461 (Selleckchem).
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5

Validating IDH Mutant Compound Screens

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Drug screening was done using IDH inhibitors AGI-5198 (Agios) or BAY-1436032 (Bayer) or the FDA-approved Oncology Drug Set II library (National Cancer Institute) containing 107 compounds. The compounds Gemcitabine hydrochloride (Sigma-Aldrich), Paclitaxel (Sigma-Aldrich), Teniposide (Santa Cruz Biotechnology, Inc), Daunorubicin hydrochloride (SelleckChem), Romidepsin (MedChemExpress), Dactinomycin (BioViotica), Regorafenib (MedChemExpress), Omacetaxine mepesuccinate (Sigma-Aldrich), and Marizomib (Sigma-Aldrich), were selected for the validation studies. Initial NIH compound screens were carried out in a 96-well format on 7 IDH mutant cultures and validation studies were performed in 384-well plates on all 12 IDH mutant cultures using the STARlet automated pipetting system (Hamilton). Serial dilutions of the selected compounds were added after 24 hours and viability was assessed by CellTiter GLO 2.0 after five days. For details see Supplementary Methods.
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6

Marizomib Treatment for GBM Edema

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Marizomib (Sigma-Aldrich) was diluted in a 2X concentration in E3/H containing 10 µM dexamethasone, the standard treatment to reduce edema in GBM,32 (link) and added in 100 µL to embryos (to a final concentration 0.2 µM, total volume of 200 µL). Controls contained identical concentrations of DMSO (0.02%) and dexamethasone.
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7

Peptide FRET Substrates for Protease Assays

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Peptide FRET substrates with ten glutamine residues were procured from GenScript (Piscataway, NJ, USA); the substrate with five glutamine residues was purchased from Peptide Protein Research Ltd. (Fareham, UK). The standard fluorescent substrates for proteasome assays (N-succinyl-Leu-Leu-Val-Tyr-7-amino-4-methylcoumarin, Suc-LLVY-AMC) and HIV protease substrate 1 (Arg-Glu(EDANS)-Ser-Gln-Asn-Tyr-Pro-Ile-Val-Gln-Lys(Dabcyl)-Arg) were from Sigma-Aldrich (St. Louis, MO, USA) and Invitrogen (Carlsbad, CA, USA), respectively. Ac-RLR-AMC and Z-LLE-AMC were from UBPBio (Dallas, TX, USA). Bortezomib was from LC Laboratories (Woburn, MA, USA), MG-132 (Z-LLL-CHO), leupeptin (as hemisulfate salt), and marizomib was from Sigma-Aldrich, and Z-P-nLeu-D-CHO was from Enzo Life Science (Farmingdale, NY, USA). All other reagents were of the highest quality available or for molecular biology grades and were used without additional purification.
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8

Primary human pulmonary artery smooth muscle cell culture

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Primary human pulmonary artery smooth muscle cells (HPASMCs) were obtained from ScienCell Research Laboratories (ScienCell Research Laboratories, Carlsbad, CA, USA) and were cultured in a smooth muscle cell medium (cat. #1101, ScienCell Research Laboratories, Carlsbad, CA, USA) supplemented with 2% fetal bovine serum, 1% smooth muscle cell growth supplement, and 1% penicillin–streptomycin in a humidified incubator at 37 °C containing 5% CO2. HPASMCs were passaged at 70% to 80% confluence by dissociation from plates with 0.25% trypsin–EDTA and passages 5 to 12 were used in the experiment. When performing hypoxia experiments, HPASMCs were incubated under 1% Oxygen. The concentration of oxygen was controlled by an oxygen controller (model ProOx 110, BioSpherix Ltd., Redfield, NY, USA), which senses oxygen inside the chamber and infuses either nitrogen to reduce the concentration or oxygen to raise the concentration. Cobalt chloride (CoCl2), bortezomib, and marizomib were purchased from Sigma-Aldrich Inc. (St. Louis, MO, USA).
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9

Proteasome and Autophagy Inhibitors

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Ac-nLPnLD-amc, Boc-LSTR-amc and Suc-LLVY-amc peptides were purchased from Bachem AG (Bubendorf, CHE). Marizomib, chloroquine and verteporfin were from Sigma (St. Louis, MO), bortezomib was from Tebu bio (Le Perray en Yvelines, France), bafilomycin A1 and everolimus were from Invivogen (San Diego, CA, USA).
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