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89 protocols using gdc 0941

1

Apoptosis Induction by Vemurafenib and GDC-0941

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Cells were plated at 60% confluency and allowed to attach overnight in 6-well plates. Cultures were then treated with vehicle, 3µM vemurafenib, 3µM GDC-0941 (Selleck) or the combination of 3µM vemurafenib and 3µM GDC-0941 for 72 hours. Annexin V and TMRM staining was performed as previously described in [24 (link)].
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2

Silencing Kinases and Phosphatases

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Cells were transfected with siRNAs using the Lipofectamine RNAiMax transfection reagent (13778150, Thermo Fisher Scientific) following the manufacturer’s protocol. Cells were transfected with 24–72 nM siRNA in transfection medium supplemented with 2% charcoal-stripped FBS (12676-029, Gibco, Thermo Fisher Scientific) for 24-48 hours before replacing with fresh growth medium. Proteins were harvested from cells 72 hours after transfection unless otherwise stated. The siRNAs used in this study were nontargeting siRNA (siCTRL, D-001810-10-20, Dharmacon), WNK1 targeting siRNA (siWNK1, L-005362-02-0005, Dharmacon), MTOR targeting siRNA (siMTOR, L-003008-00-0005, Dharmacon), and PPP2R1A targeting siRNA (siPPP2R1A, L-060647-00-0005, Dharmacon). AKT and MTOR inhibitors GDC0941 and rapamycin (S1065 and S1039, respectively, Selleckchem) were dissolved in DMSO, and cells were treated with 5 μM GDC0941 and 10–40 μM rapamycin for 24 hours, while the control cells received equivalent volumes of DMSO.
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3

Inhibiting PI3K Signaling in CTCL

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PIKP110a inhibitors, PIK75, A66, GDC0941, and BEZ235 are from Selleck (Houston, TX). Isolation of PBMCs or CD4+ T cells from both patients and healthy donors and culture of CTCL cell lines (Hut78, HH, and H9) were performed as previously described (Bliss-Moreau et al., 2015 (link)). All patient tissue collection and research use adhered to protocols approved by the institutional review and privacy boards at City of Hope, in accordance with the Declaration of Helsinki. All participants signed written informed consent.
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4

Metabolic Regulation by Pharmacological Inhibitors

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15N-labelled glutamine (Cambridge Isotope Laboratories NLM-557-0.5), D-glucose (Sigma G7528), L-glutamine (Sigma G3126), AZD8330 (Selleckchem, S2134), trametinib (Selleckchem, S2673), GDC0941 (Selleckchem, S1065), leflunomide (Sigma L-5025), brequinar sodium salt (Sigma, SML0113), uridine (Sigma, U3003), inosine (Sigma, I4125), mitochondrial stress kit (Seahorse 101706-100), VECTASTAIN Elite ABC Kit (pk-6100; Vector Labs), DAB (sk-4100; Vector labs).
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5

Melanoma Cell Line Cultivation and Drug Preparation

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All melanoma cell lines were obtained from the Massachusetts General Hospital Cancer Center. C32, K2, MMACSF, SKMEL28, and WM115 cell lines were grown in DMEM/F12 (Invitrogen) supplemented with 5% fetal bovine serum (FBS) and 1% sodium pyruvate (Invitrogen). COLO858, LOXIMVI, MZ7MEL, RVH421, and WM1552C cell lines were grown in RMPI 1640 (VWR) supplemented with 5% fetal bovine serum (FBS) and 1% sodium pyruvate (Invitrogen). We added penicillin (50 U/ml) and streptomycin (50 μg/ml) to all growth media.
Chemical inhibitors from the following sources were dissolved in dimethyl sulfoxide (DMSO) as 10 mM stock solutions for in vitro studies: vemurafenib (PLX4032), PLX4720, SB590885, selumetinib (AZD6244) and AZ628 (all from MedChem Express), JNK-IN-8 (EMD Millipore), SP600125, doramapimod (BIRB796), and SB202190, GDC0941, tofacitinib (CP-690550), and IKK16 (all from Selleck Chemicals).
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6

PI3K Inhibitor Treatment Profiling

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293T and IGROV cells were plated at 5 × 105 cells per 10 cm plate, and were treated with PI3K inhibitors GDC-0941 and PI-103 (Selleck Chemicals, Houston, TX) 24 hours post plating. Following 24 hours of treatment, cells were harvested as above and subjected to western blot analysis.
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7

Anticancer Inhibitor Compound Preparation

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The HDACi (LBH589, SAHA and FK228) were purchased from Selleck Chemicals, Munich, Germany. The MAPK inhibitors, GSK1120212 and ARRY-162, were obtained from Selleck Chemicals and AbMole BioScience, HongKong, China, respectively. FAK inhibitor TAE226 was from Selleck Chemicals and PF573228 was from Tocris Bioscience, Bristol, UK. Phosphatidylinositol 3-kinases (PI3K) inhibitors GDC-0941 and BKM120 were obtained from Selleck Chemicals. All compounds were dissolved in dimethyl sulfoxide and stock drug solutions were diluted in complete RPMI-1640 culture medium (Life Technologies, Mulgrave, VIC, Australia) to various concentrations for experimentation.
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8

Stable and Transient Cell Line Generation

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Cell lines (ATCC) were grown in DMEM (Life Technologies) with 10% FBS (Hyclone). MCF-7 and T47D cells stably expressing shRNA targeting PTEN or mismatch control (shMM) were described previously [41 (link)]. Generation of other stable Cell lines is described in Supplementary Methods. In transient transfection experiments, cells were transfected with pcDNA plasmid encoding myc-PREX1-HA (from Atanasio Pandiella, CSIC-Universidad de Salamanca) or FLAG-HA control (Addgene) plus Lipofectamine 2000. Cells were transfected with siRNA targeting P-REX1 or AllStars Negative Control (Qiagen, Dharmacon) plus Lipofectamine RNAiMAX (Life Technologies). Cells were treated with IGF-1 (PeproTech), heregulin (HRG), BKM-120, GDC-0941, MK-2206 (Selleckchem), or EHT1864 (Tocris Bioscience) as indicated in figures.
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9

Evaluating Kinase Inhibitors in DLBCL

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The chemical SYK inhibitor, R406, was a gift from Rigel Pharmaceuticals (San Francisco, CA, USA). R406 was dissolved in DMSO at a concentration of 10 mM and stored at −80°C. For immediate inhibition, cells were incubated with 1 μM R406 or vehicle alone (in PBS) in a 37°C water bath for 2 hours (h). For long-term inhibition, R406 was added to cell culture medium at a final concentration of 1 μM and cells were maintained in an incubator at 37°C for 24 h. The chemical pan-PI3K inhibitor, LY294002, was purchased from Sigma-Aldrich (Saint Louis, MO, USA), The chemical SYK inhibitor, GS-9973 (entospletinib), the PI3K isoform-predominant inhibitors, GDC-0941 (pictilisib, PI3K α/δ>β/γ), CAL101 (idelalisib, d) and IPI145 (duvelisib, δ/γ) and the BTK inhibitor, PCI-32765 (ibrutinib) were purchased from Selleckchem (Houston, TX, USA). DLBCL cell lines were treated with GS-9973 (2 μM), LY294002 (10 μM), GDC-0941 (0.5 μM), CAL101 (2 μM), IPI145 (1 μM), PC1-32765 (0.1 μM) or vehicle (DMSO) for 24 h as previously described.9 (link) The doses of SYK, PI3K and BTK inhibitors used in these studies were determined based on prior analyses of the respective agent EC50s of these agents;9 (link) the LY294002 dose was chosen based on previously reported studies.3 (link),16 (link) Following treatment with chemical SYK, PI3K or BTK inhibitors, cells were harvested for additional analyses (below).
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10

Cell Line Characterization and Compound Screening

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T47D, MCF7 cells were purchased from American Type Culture Collection (ATCC) in 2012 - 2015. They were authenticated using STR testing and tested negative for Mycoplasma contamination. EFM19, BT474, MDAMB453, HCC202, MDAMB361, HCC1419, MDAMB415, HCC1937, CAL51, BT20, HCC1954, and JIMT1 cells were purchased from Cancer Cell Line Encyclopedia (CCLE) at the Broad Institute in 2015-2016, and were authenticated using SpectroCHIPII-G384 by Sequenom's MassARRAY Analyzer Compact. All the cells were maintained in RPMI-1640 with 10% fetal bovine serum. BYL719, GDC0941, BKM120, AZD1208, GDC0032, PI-103, BX795, BX912, MK2204, GDC0068, sirolimus, everolimus, PP242 and WYE were purchased from Selleck Chemicals (Supplementary Material and Methods). Blasticidine was purchased from Life Technologies. LGH447 was obtained from Novartis.
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