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10 protocols using gdc 0623

1

Radiolabeled ICF01012 and MEK Inhibitors

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[131I] iodine was purchased from Perkin Elmer (Waltham, MA, USA) or Izotop (Budapest, Hungary). Radiolabeling of ICF01012 was performed as previously described [23 (link)]. For the [131I]ICF01012 alone experiments, each spheroid was irradiated at day 6 of culture with 37 kBq of [131I]ICF01012/100 µL of cell culture medium (without FCS). The addition of medium alone was used as a control. After 1 h of incubation, the irradiation medium was removed and replaced by complete medium supplemented with 0.5% methylcellulose. For the [131I]ICF01012 and MEK inhibitors (MEKi) combinations, each spheroid was pretreated for 2 h with cobimetinib (GDC-0973) (Selleckchem (Houston, TX, USA), 100 nM, SK-MEL-3 spheroids), GDC-0623 (Selleckchem, 50 nM, B16F10, and NRAS 1007 spheroids), or dimethyl sulfoxide (DMSO) (control and [131I]ICF01012 alone groups) on day 6 of culture. Then, each spheroid was irradiated according to the above-mentioned protocol with cell culture medium containing the corresponding MEKi (MEKi alone or TRT + MEKi groups) or DMSO (control DMSO or TRT alone groups). Spheroids were then incubated from 1 to 72 h.
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2

Cell Viability Assay Using SRB

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Cells were seeded at a density of 2000 cells per well in 96 well plates. Twenty hours after seeding the medium was changed and 48 h after seeding (day 0) the cells were treated with 1 μM of DMSO or inhibitor(s) for three days. After completion of the drug exposure, cells were analyzed using the sulforhodamine B (SRB) colorimetric assay as described [38 (link)]. The relative cell growth was calculated on the average OD of the sample versus/normalized to average OD at day 0 and OD of the vehicle (DMSO)-treated control.
Inhibitors used in our study were: RO5126766 (CH5126766) (Selleckchem, Houston, TX, USA, S7170), GDC-0623 (Selleckchem, Houston, TX, USA, S7553), SCH772984 (Selleckchem, Houston, TX, USA, S7101). All inhibitors were dissolved in DMSO (D1435, Sigma Aldrich, St. Louis, MO, USA) and used at 1 μM final concentration. Final DMSO concentration was kept at 0.1% or below in control and inhibitor-treated cells for single treatments and between 0.2% and 0.3% in control and inhibitor-treated cells for double and triple treatments respectively.
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3

Subcellular Fractionation of Cell Lines

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Cycloheximide was purchased from Santa Cruz Biotechnology (Dallas, TX, USA)
Subcellular fractionation was achieved using the Subcellular Protein Fractionation Kit for Cultured Cells according to manufacturer’s protocol (Thermo Fisher Scientific, Waltham, MA, USA). Vemurafenib (PLX4032), dabrafenib (GSK2118436), sorafenib (BAY 43–9006), regorafenib (BAY 73–4506), RAF265 (CHIR-265), selumetinib (AZD6244), trametinib (GSK1120212), PD0325901 and GDC0623 were purchased from Selleckchem (Houston, TX, USA). PLX8389 (also called paradox-breaker or PB-3) was generously provided by Plexxikon (Berkeley, CA, USA).
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4

Studying Necrotic Supernatant Effects

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RTECs were grown to 70% confluency in 12 well biocoat plates (Becton Dickinson, Bedford MA). One hour prior to stimulation, the growth media was removed and replaced with fresh DMEM:F12 or 1000nM MEK1 inhibitor GDC0623 (Selleckchem, Cat #S7553) dissolved in DMEM:F12. After 1 hour, the media was replaced with DMEM:F12, necrotic supernatant, or necrotic supernatant+MEK1 inhibitor and the cells placed back in the incubator for 3 hours. After 3 hours, cells were washed twice with 2mL of sterile PBS and 300uL of RNA lysis buffer (Zymo Research, Irvine CA) was added directly to the plates. Lysates were stored at −80 until processing.
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5

Assessing Long-term Drug Resistance

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Long-term drug resistance was assessed by seeding in parallel 2.5 × 105 and 5 × 105 cells in 6-cm plates and 24 h after plating cells were treated with 1 μM of a particular inhibitor as single or double treatment. For the plates where the initial cell number was 2.5 × 105, medium and inhibitor(s) were changed every 3 days for 14 days. Cells were fixed and stained with Crystal Violet solution, pictures were captured with EPSON PERFECTION V300 PHOTO scanner and images acquired with the paired software. taken. For the plates whose initial cell number was 5 × 105, medium and inhibitor(s) were changed every 3 days until plates were fully confluent. At confluence plates were split 1:5 to one 6-cm-plate without inhibitor(s) (1/5), in order to test for possible drug addiction, a 10-cm-plate with inhibitor(s) (3/5) for expansion/freezing and one 6-cm-plate with inhibitor(s) (1/5) for future protein isolation. Days after resistance were counted from the splitting time until the plates reached confluence again. Inhibitors used were RO5126766 (CH5126766) (Selleckchem, Houston, TX, USA, S7170), GDC-0623 (Selleckchem, Houston, TX, USA, S7553), SCH772984 (Selleckchem, Houston, TX, USA, S7101), LY3214996 (Selleckchem, Houston, TX, USA, S8534). Final DMSO concentration was kept at 0.1% in control and inhibitor-treated cells for single treatments and 0.2% for double treatments.
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6

Solubility and Formulation of BI-847325 and GDC-0623

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BI-847325 and GDC-0623 (Selleckchem) were dissolved in DMSO and diluted in medium for use in in vitro experiments. For the in vivo experiments, BI-847325 was solubilized in 1% 2-hydroxyethyl cellulose, polysorbate 80, with the pH adjusted to 2.8 with 1 mol/L HCl.
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7

PDAC Cell Line and PDX Characterization

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IMR90 and human PDAC cell lines HPAC, 8988T, PaTu8902, Miapaca2, DanG,
S2013, and PANC1 were purchased from American Type Culture Collection (ATCC).
PDX148 was established from PDX tumors (20 ). IMR90 was grown in Eagle’s Minimum Essential Medium with
10% FBS. The PDAC cell lines and PDX148 cells were cultured in RPMI1640
supplemented with 10% FBS. All the cell lines were tested negative for
mycoplasma (LookOut Mycoplasma PCR Detection Kit) throughout the study. Cells
were kept in culture for a maximum of 15 passages after recovery from frozen
vials. Trametinib, SCH772984, BKM120, GDC-0623, gemcitabine, and paclitaxel were
purchased from Selleckchem. 4-Phenylbutyric Acid (4-PBA) and 2DG were obtained
from Sigma Aldrich. Heptelidic Acid was purchased from Cayman Chemical and
R-GNE-140 was purchased from Medkoo Bioscience. POMHEX was provided by Dr.
Florian L. Muller at MD Anderson Cancer Center.
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8

Isolation and Characterization of Primary Rat Osteoblasts

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Primary osteoblasts were isolated from the calvaria of neonatal Sprague-Dawley (SD) rats (SIPPR-BK Inc., Shanghai, China) and digested using 0.1% collagenase type I in DMEM medium (Sigma-Aldrich, Saint Louis, MO, USA) in a shaking bath at 37°C for 60 min. Osteoblasts were cultured in Dulbecco's Modified Eagle's Medium (DMEM, Biowest, France) supplemented with 10% fetal bovine serum (FBS, Biowest, France). Osteoblasts at passage P1 were used for phenotypic and functional studies. To assess protein phosphorylation levels, osteoblasts were cultured in DMEM plus 0.1% FBS overnight and treated with 20 ng/ml IL-1β (RD company) or IL-1β plus 0.1 μM GDC0623 (Selleck, China) or IL-1β plus 5 μM C188-9 (Selleck, China) for 60 min.
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9

Isolation and Characterization of Glioblastoma Stem Cells

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GSCs were isolated from patient-derived surgical specimens at the University of Texas MD Anderson Cancer Center, as previously described,27 (link) and approved by the institutional review board (protocol #LAB04-0001). The GSCs were grown and maintained in suspension culture in Dulbecco’s modified Eagle medium (DMEM, Corning, NY, USA), supplemented with 2% B-27 (Thermo Fisher Scientific, Waltham, MA, USA), epidermal growth factor (EGF), basic fibroblast growth factor (FGF), and antibiotics at 37°C in a 5% CO2 atmosphere, as described previously.28 (link) Short tandem repeats using the Applied Biosystems AmpFISTR identifier kit (Foster City, CA, USA) were used to authenticate cells. All the GSCs lines used in this study are isocitrate dehydrogenase wild-type (IDHwt) except GSC5-22. The EGFR amplification in GSCs lines was characterized as described in the previous study.29 (link) All MEK inhibitors (GDC-0623, MEK162, RO5126766 [RO5], and trametinib) were purchased from (Selleckchem, Houston, TX, USA). All cell lines tested negative for mycoplasma contamination using the MycoAlert Detection Kit (Lonza, Houston, TX, USA).
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10

Protein Extraction and Western Blotting

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Cells were plated at 1x106cells/ml in presence of serum and then serum starved for 24 hours. Cells were exposed to indicated concentrations of drug for 1 hour and then lysed with RIPA lysis buffer (50 mM Tris, 150 mM NaCl, 0.1% SDS, 0.5% sodium deoxycholate, 1% Nonidet P-40, Roche complete protease inhibitor mixture tablets, and 100x Pierce phosphatase inhibitor mixture) while being maintained at 4°C. Cell suspension was centrifuged and clarified lysates isolated. Lysates were protein quantified and diluted to a standard concentration with 2X LDS buffer so all aliquots had the same protein quantification prior to western blotting. Trametinib was provided by GlaxoSmithKline. PLX8394 was provided by Plexxikon. Selumetinib, binimetinib, GDC0623, and cobimetinib were purchased from Selleck Chemicals (Selleckchem.com). Drug studies in soft agar assays were performed as described previously [4 (link)].
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