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92 protocols using ponatinib

1

Cell Cycle and Invasion Assays for Targeted Therapies

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For the treatment of TRZ, each cell was seeded on 6-well plates and after 24 h, TRZ was treated to the cells at 50 μg/mL for 48 h. The cell cycle was analyzed by flow cytometry. For the treatment of ponatinib and sunitinib, each cell (2 × 103 cells/well) was seeded on 96-well plates and after 24 h, ponatinib (Selleck Chemicals, Houston, TX, USA), sunitinib (Selleck Chemicals), or S3I-201 were treated at the indicated concentration for 48 h and for 10 days. In the cell invasion assay, each cell was seeded in the Boyden-chamber inserts with or without 1 μM pontatinib or sunitinib for 24 h. Phosphate-buffered saline was treated as a vehicle control for TRZ treatment and dimethyl sulfoxide was treated as a vehicle control for inhibitors including ponatinib, sunitinib, and S3I-201.
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2

Anticancer Drugs Combination Treatment

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Doxorubicin hydrochloride (#D1515), vincristine, and insulin growth factor 2 (IGF2, #I2526) were purchased from Merck. Irinotecan (#S2217), MK-2206, capivasertib (AZD5363), alpelisib (HY-15244), nilotinib (S1033), pazopanib (S3012), and ponatinib (S1490) were purchased from Selleckchem. Everolimus (RAD001, SRP020750e) was purchased from Sequoia Research Products, etoposide was purchased from Sandoz and AVE 1642 from Immunogen. D-188514, an ifosfamide analog that does not require metabolic activation, was purchased from Niomech. The PI3K/mTOR dual inhibitor NVP-BEZ235 was kindly provided by Novartis. Trabectedin (ET-743) was kindly provided by PharmaMar. Working dilutions of all drugs were prepared immediately before use.
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3

Cell Culture Materials and Reagents

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RPMI 1640 medium and penicillin/streptomycin were purchased from Lonza (Verviers, Belgium), amphotericin B from PAN-Biotech (Aidenbach, Germany), fetal calf serum (FCS) from Life Technologies (Carlsbad, CA) and venetoclax, ponatinib, and selinexor from Selleckchem (Houston, TX). Gemtuzumab-ozogamicin (GO) was obtained from Pfizer (New York, NY). Stock solutions of drugs were prepared by dissolving in dimethylsulfoxide (DMSO) (Sigma Aldrich, St. Louis, MO). 3H-thymidine was purchased from Perkin Elmer (Boston, MA). A specification of monoclonal antibodies (mAb) used in this study is shown in Supplementary Table S1.
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4

Metabolic Modulators for Cell Line Screening

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Ponatinib, Bazedoxifene and Lopinavir were purchased from Selleck Chemicals (Houston, TX, USA). 2-Deoxy-D-glucose (2-DG), O-benzyl-L-Serine (BenSer), 6-diazo-5-oxo-norleucine (DON), bis-2-(5-phenylacetamido-1,2,4-thiadiazol-2-yl)ethyl sulfide (BPTES), Telaglenastat (CB-839), epigallocatechin gallate (EGCG), 2-allyl-1-hydroxy-9,10-anthraquinone (R162), L-buthionine-sulfoximine (BSO), L-glutamine, glutamic acid and dimethyl 2-oxoglutarate were all purchased from Sigma (Sigma-Aldrich, St. Louis, MO, USA). The caspase-3 fluorescence dye was from Sartorius (Sartorius AG, Göttingen, Germany). Human IL-11Rα and negative control siRNA were from Thermofisher Scientific (Scoresby, VIC, Australia).
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5

Creatine Uptake Regulation by Drugs

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Approximately 15 × 106 cells were grown and exposed to different drugs to examine the regulation of creatine uptake. Fewer cells, approximately 2 × 106, were used in experiments for immunoblot analyses. Drug dose-response experiments were initially performed with different compounds to determine the effective concentrations. For ouabain, cells were incubated in increasing concentrations, starting at 1.0 nM and increased by order of 10 until the concentration of 10 μM was achieved. Separate populations of the cells were also treated with dasatinib or ponatinib (Selleckchem), dual Bcr-Abl and Src family tyrosine kinase inhibitors. The creatine competitive inhibitor, 3-Guanidinopropionic Acid (Sigma-Aldrich, St. Louis, MO), was reconstituted in media (above) and a 30-mM concentration used to treat Myl-R cells. Cells were treated for 24 hours before metabolite extraction. The drugs/compounds were reconstituted in incubation media (3-Guanidinopropionic Acid), hot, autoclaved water (ouabain), and DMSO (imatinib, ponatinib, dasatinib); likewise incubation media, diH2O, and DMSO were also used as the vehicle controls.
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6

Bcr-Abl Inhibitors in Leukemia

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Ba/F3 cells expressing Bcr-AblWT and Bcr-AblT315I were obtained from Dr. Shah’s laboratory (UCSF, San Francisco, CA, USA). The cells were maintained in RPMI 1640 (Corning) supplemented with 10% fetal bovine serum (v/v, HyClone, ThermoScientific) and 1× penicillin, strepatmycin, and glutamine (GE Healthcare) at 37 °C and 5.0% CO2. Imatinib and ponatinib were purchased from Selleckchem. Dimethyl sulfoxide (DMSO) was purchased from Sigma-Aldrich (St. Louis, MO, USA). The following antibodies were purchased from Cell Signaling (Boston, MA, USA): anti-Abl, anti-phospho-Abl (Y412), anti-phospho-STAT5 (Tyr694), and anti-STAT5. Anti-actin antibody was purchased from Sigma-Aldrich (St. Louis, MO, USA). Anti-mouse secondary antibody was purchased from Jackson ImmunoResearch Laboratories (West Grove, PA, USA), whereas anti-rabbit secondary antibody was obtained from Abcam (Cambridge).
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7

Screening Library and Inhibitor Assay

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The screening library (1,154 FDA approved drugs), GDC-0994 (S7554), Crenolanib (CP-868596), MGCD-265 (S1361), LY2874455 (S7057), PP2 (S7008), GDC-0994 (S7554) and Ponatinib (S1490) were purchased from Selleck. SP600125 (HY-12041), SB203580 (HY-10256) were purchased from MedChem Express. Actinomycin D (A4262), B27 (17504044) and EGF (100-47) were purchased separately from Sigma, Invitrogen and Peprotech. All chemicals were dissolved in dimethyl sulfoxide (DMSO) for in vitro studies.
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8

Breast Cancer Cell Colony Formation

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For the colony formation assays, BT474 TRZ_R and HCC1954 breast cancer cells were plated into 6-well plates (2 × 103 cells/well) and incubated at 37 °C, O/N. The next day, the cells were treated with 2 μM ponatinib or sunitinib (Selleck Chemicals) and then incubated for an additional 10 days. Cell colonies were fixed with 10% ethanol, stained with 0.01% crystal violet, and observed using a CK40 inverted microscope (Olympus, Tokyo, Japan).
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9

Cell Viability Quantification by Luminescence

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To determine cell viability, cells were seeded in 96 well plates at a density of 4 × 103 cells per well. After a recovery time of 24 h, the cells were exposed to diverse compounds at different drug concentrations in triplicates. The small molecule inhibitors ponatinib, nintedanib, AZD-4547, dovitinib, erdafitinib, avapritinib, and dasatinib were purchased from Selleck Chemicals (Houston, TX, USA). Upon 72 h incubation, cell survival was determined with the commercially available CellTiter-Glo® Luminescent Cell Viability Assay (Promega, Madison, WI, USA) according to manufacturer’s instructions and luminescence signals were measured with the Tecan infinite 200Pro (Zurich, Switzerland). Dose–response curves were generated and anti-cancer activity was expressed as IC50 values calculated by GraphPad Prism 8.0.1 (GraphPad Software, La Jolla, CA, USA) using point-to-point function.
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10

Characterization of CML Cell Lines

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Human CML cell lines, K562 (kind gift from Dr. Junia Melo), KU812 (kind gift from Dr. S Tiong Ong) and murine CML cell lines, 32Dp210 (kind gift from Dr. Brian Druker) and 32Dp210 T315I mutant (kind gift from Dr. James Griffin) were maintained in suspension in RPMI medium (Thermo Fisher Scientific, USA), supplemented with 10% fetal bovine serum, 4 mM L-glutamine (Hyclone, USA), 1% penicillin/streptomycin (Gibco, Thermo Fisher Scientific, USA). 32Dp210 and 32Dp210 T315I are murine hematopoietic 32D cells transfected with BCR-ABL1 and T315I mutant respectively [18] (link). The cell lines used in our study are validated with short tandem repeat (STR) profile analysis or Sanger sequencing analysis (Table S1 and Figure S1). Imatinib (LC Laboratories, USA) and ponatinib (Selleckchem, USA) were dissolved in sterile distilled water. Mefloquine hydrochloride (Sigma, US) and bafilomycin A1 (Cayman Chemicals, USA) were reconstituted in dimethylsulfoxide (DMSO; Sigma, USA). N-acetyl cysteine (NAC; Sigma, USA) was dissolved in sterile distilled water. α-Tocopherol (Sigma, USA) was dissolved in a mixture of DMSO and 30% ethanol.
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