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6 protocols using lenalidomide

1

Kinetic Analysis of NPM1 Binding

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We determined the binding kinetics by a surface plasmon resonance (SPR) analysis with the Biacore 3000 system (GE Healthcare, Buckinghamshire, UK). All experiments were performed at 25°C using TBS buffer (25 mM Tris-HCl, pH 7.4, 137 mM NaCl, 3 mM KCl). Recombinant NPM1 was expressed in E. coli and purified. The NPM1 obtained (1.84 µM, 100 µL) was immobilized onto the sensor chip NTA (GE Healthcare). The measurements were performed under conditions of 662 resonance units of the ligand and at a flow rate of 30 µL/min. To determine the dissociation constants, we injected three different concentrations of TC11 and lenalidomide (Santa Cruz Biotechnology, Santa Cruz, CA). The injection periods for association and dissociation were 60 and 300 s, respectively. The binding data were analyzed with 1:1 binding with the mass transfer model in the BIA evaluation software ver. 4.1 (Biacore).
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2

Thymic Cell Culture and Compound Screening

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Thymic cells were cultured as described (35 (link)). Briefly, enzymatically dispersed thymic cell suspensions were washed (and some aliquots irradiated with 1,250 rads from a 60Co source) and cryo-stored within a few hours of thymectomy. Subsequently, they were thawed carefully, and cultured at 6× 105 - 1× 106 cells per well in 96 well round-bottomed plates, without added stimulants, in 200 μL of RPMI medium containing 15% fetal bovine serum (Bodinco, the Netherlands), 50 U/mL penicillin, 50 U/mL streptomycin and 1 mM sodium pyruvate, at 37°C in humidified air with 5% CO2. Every 2 - 3 days, we removed (and stored) 90 μL of supernatant from each well, and replaced it with 100 μL of fresh medium ± any test drugs. Thymic cells were pre-cultured for 3 - 7 days, to allow recovery from the thawing procedure, adaptation to culture conditions and for measuring baseline Ab production before addition of test drugs.
We dissolved lyophilized bortezomib (Velcade, Janssen-Cilag B.V., Belgium) in sterile saline, dexamethasone (D4902; Sigma-Aldrich) in absolute ethanol, and lenalidomide (Santa Cruz Biotechnology; sc-218656) in dimethyl sulfoxide.
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3

Cytotoxicity and Apoptosis Assay Protocol

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Cytotoxicity of the compounds was analyzed by Cell Counting Kit-8 (Dohjin Chemicals, Kumamoto, Japan) or trypan blue dye exclusion assay according to the manufacturer's protocol. The MEBCYTO Apoptosis kit was used to detect apoptosis by flow cytometry using FACSVerse (BD Biosciences, Franklin Lakes, NJ, USA) according to the manufacturer's protocol. Melphalan and lenalidomide were purchased from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA, USA) and Sigma-Aldrich; Merck KGaA, (Darmstadt, Germany), respectively. A pan-caspase inhibitor, ZVAD-fmk (Medical and Biological Laboratories, Nagoya, Japan), was utilized in some experiment at a concentration of 32 nM.
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4

Cytarabine storage and epigenetic compound libraries

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Cytarabine (147–94-4, Pfizer, New York, NY, USA) was aliquoted and stored at 4 °C with bulk concentrations of 411 mM. SCREEN-WELL® Epigenetics library (BML-2836, Enzo LifeSciences Inc., Farmingdale, NY, USA) and Chemotherapeutic Agent Library (L1500, Selleck, Munich, Germany) were stored at − 80 °C until use. Substances used for proliferation studies including bortezomib (2204S, Cell Signaling Technologies), lenalidomide (PCID-216326 Santa Cruz Biotechnology, USA), apicidin (A8851, Sigma Aldrich), belinostat (PXD101), M-344 (M5820, Sigma Aldrich), oxamflatin (O3139, Sigma Aldrich, St. Louis, MO, USA), scriptaid (S7817, Sigma Aldrich), trichostatin A (T1952, Sigma Aldrich) and vorinostat (SAHA MK0683, Selleck) were dissolved in DMSO (Sigma Aldrich), aliquoted and stored at − 80 °C until use.
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5

Solubilization of Anticancer Compounds

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Melphalan (Sigma-Aldrich), lenalidomide (Santa Cruz Biotechnology, Dallas, TX, USA), panobinostat (Selleck Chemicals, Houston, TX, USA), bortezomib (Selleck Chemicals), and carfilzomib (Amgen, Thousand Oaks, CA, USA) were dissolved in dimethyl sulfoxide (DMSO) (Sigma-Aldrich) and kept frozen at −20 °C. Dexamethasone (MSD, Tokyo, Japan) was stored at 4 °C until use. Thapsigargin (Wako, Osaka, Japan), PERK inhibitor (GSK2606414; Selleck Chemicals) and IRE1α inhibitor (STF083010; Sigma-Aldrich) were also dissolved with DMSO and stored at −20 °C.
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6

Combination Immunomodulatory Drug Protocol

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The following reagents were purchased from the indicated manufacturers: panobinostat (LBH589) and ACY-1215 from Cayman Chemical Company (MN, USA); entinostat (MS-275) from Selleck (Houston, USA); lenalidomide from Santa Cruz Biotechnology (CA, USA); pomalidomide from Toronto Research Chemicals (Toronto, Canada); recombinant human (rh) IFN-γ from R&D systems (MN, USA); rh IL-6 from Pepro Tech Inc. (London, UK) and MG132 from Selleck (Houston, USA); phycoerythrin (PE)-conjugated monoclonal antibodies (mAbs) against human PD-L1 (#329706), human MICA/MICB (#320906), human CD119 (IFN-γR1) (#308606) and mouse IgG1-κ isotype control (#400114) from BioLegend (CA, USA); human ULBP-2/5/6 (FAB1298P) from R&D systems (MN, USA); fluorescein isothiocyanate (FITC)-conjugated mAbs against human CD38 (#555459) from BD Biosciences (CA, USA); anti-phosho-STAT1 (Tyr701) antibody (#7649), anti-STAT1 antibody (#14995), anti-PD-L1 antibody (#13684) and anti-GAPDH antibody (#5174) from Cell Signaling; anti-IRF1 antibody (sc-497) from Santa Cruz (CA, USA); and anti-β-actin antibody (A5316) from Sigma-Aldrich (St. Louis, MO, USA); 17-AAG from Calbiochem EMD Biosciences, Inc. (La Jolla, CA, USA).
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