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6 protocols using torin1

1

Multi-omics Profiling of Cell Signaling

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Human IFN-γ and S7 micrococcal nuclease were purchased from Roche; human M-CSF was from Peprotech; Pam3CSK4 was from EMC Microcollections; UltraPure E.Coli LPS was from Invivogen. MG132, CGP57380, Rapamycin and PP242 were purchased from Calbiochem; Cycloheximide, Bafilomycin A1, 1-Methyl-D-tryptophan (1-D-MT), L-Tryptophan and 10058-F4 were from Sigma; Torin 1 was from R&D Systems; LY 294002 was from EMD Millipore. The following antibodies were purchased from Cell Signaling: mTOR (#2983), p-TSC2(Thr1462) (#3617), TSC2 (#4308), p-Akt (Ser473) (#4060), p-p70S6K(Thr421/Ser424) (#9204), 4E-BP1 (#9644), p-4E-BP1(Thr37/46) (#2855), LC3A (#4599), LC3B (#3868), IκB-α (#9242), Mnk1(#2195), p-Mnk1(Thr197/202) (#2111), eIF4E (#9742), p-eIF4E(Ser209) (#9741), p-p38(Thr180/Tyr182) (#9215), p-ERK1/2 (Thr202/Tyr204) (#9101), ERK (#9102), β-catenin (#9562), M-CSFR (#3152). Additionally, p38α (sc-535), HES1 (sc-25392), TBP (sc-204), LAMP1 (sc-20011) and Myc (sc-764) were from Santa Cruz Biotech. PABPC1 (ab6125), β-tubulin (ab11307) and Leucyl tRNA synthetase (ab31534) antibodies were from Abcam. mirVana miRNA isolation kit was purchased from Ambion/Life Technologies. BD™ Cytometric Bead Array (CBA) human inflammatory cytokine kit was purchased from BD Biosciences.
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2

Multi-omics Profiling of Cell Signaling

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Human IFN-γ and S7 micrococcal nuclease were purchased from Roche; human M-CSF was from Peprotech; Pam3CSK4 was from EMC Microcollections; UltraPure E.Coli LPS was from Invivogen. MG132, CGP57380, Rapamycin and PP242 were purchased from Calbiochem; Cycloheximide, Bafilomycin A1, 1-Methyl-D-tryptophan (1-D-MT), L-Tryptophan and 10058-F4 were from Sigma; Torin 1 was from R&D Systems; LY 294002 was from EMD Millipore. The following antibodies were purchased from Cell Signaling: mTOR (#2983), p-TSC2(Thr1462) (#3617), TSC2 (#4308), p-Akt (Ser473) (#4060), p-p70S6K(Thr421/Ser424) (#9204), 4E-BP1 (#9644), p-4E-BP1(Thr37/46) (#2855), LC3A (#4599), LC3B (#3868), IκB-α (#9242), Mnk1(#2195), p-Mnk1(Thr197/202) (#2111), eIF4E (#9742), p-eIF4E(Ser209) (#9741), p-p38(Thr180/Tyr182) (#9215), p-ERK1/2 (Thr202/Tyr204) (#9101), ERK (#9102), β-catenin (#9562), M-CSFR (#3152). Additionally, p38α (sc-535), HES1 (sc-25392), TBP (sc-204), LAMP1 (sc-20011) and Myc (sc-764) were from Santa Cruz Biotech. PABPC1 (ab6125), β-tubulin (ab11307) and Leucyl tRNA synthetase (ab31534) antibodies were from Abcam. mirVana miRNA isolation kit was purchased from Ambion/Life Technologies. BD™ Cytometric Bead Array (CBA) human inflammatory cytokine kit was purchased from BD Biosciences.
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3

Autophagy Induction in U2OS and MDDC Cells

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U2OS cells were obtained from ATCC. U2OS GFP‐LC3 and U2OS mRFP‐EGFP‐LC3 stable cell lines are a kind gift from Tassula Proikas‐Cezanne (Eberhard Karls University Tübingen, Germany) and Jeff MacKeigan (Van Andel Research Institute, MI, United States), respectively. All cells were grown in Dulbecco's modified Eagle's medium (DMEM; Lonza, BioWhittaker) supplemented with 10% fetal calf serum (FCS), 2 mM l‐glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin, referred to as CM. For starvation in nutrient‐depleted medium, the cells were incubated in EBSS (Gibco, Life Technologies) for 2 h. BafA1 (AH Diagnostics) was used at 100 nM and Torin1 (R&D Systems) at 50 nM.
Blood components (buffy coats) from healthy blood donors were obtained from the local blood bank (Ullevål University Hospital, Oslo, Norway) according to the guidelines of the local blood bank approved by the Norwegian Regional Committee for Medical Research Ethics. Mononuclear cells were isolated through density gradient centrifugation by using Lymphoprep (Axis Shield). MDDCs were generated through culture for 6 days in RPMI media containing 100 ng/ml granulocyte–macrophage colony‐stimulating factor (GM‐CSF; Immunotools) and 20 ng/ml IL‐4 (Invitrogen, Life Technologies) supplemented with 10% FCS, 2 mM l‐glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin.
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4

Compound-based Cell Treatment Protocol

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Compounds and growth factors used to treat cells were: Rapamycin, TGFβ, HGF (EMD Millipore, Billerica, MA), Activin (eBioscience, San Diego, CA), BMP4, Nodal, Torin1 (R&D Systems, Minneapolis, MN), Insulin, Transferrin, and Selenium (ITS) (Roche, San Francisco, CA), SU11274, AG490 (Sigma Aldrich, St. Louis, MO), and CGP57380 (Cayman Chemicals, Ann Arbor, MI). U0126 was obtained from Promega (Madison, WI). A TGFβ Type I Receptor kinase inhibitor (616451) was purchased from EMD Millipore (Billerica, MA).
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5

Modeling PI3K and KRAS Oncogenes in Breast Cells

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All cell lines were obtained from ATCC (Manassas, VA, USA) and maintained in RPMI-1640 with 10% fetal bovine serum (FBS) at 37°C and 5% CO2. Lipid-reduced FBS was made by mixing with fumed silica (20 mg/ml) (S5130, Sigma) for 3 hours. Pools of MCF10A cells stably expressing pBabe-Puro-vector, -PI3KCAH1047R (Addgene #12524)63 (link), or K-RasG12V (Addgene #9052), via retroviral transduction, were selected and cultured in DMEM-F12 with 5% horse serum, EGF (20 ng/ml), hydrocortisone (0.5 mg/ml), cholera toxin (100 ng/ml), Insulin (10 μg/ml), and puromycin (1 μg/ml) at 37°C and 5% CO2. Rapamycin (553210, Calbiochem, San Diego, CA, USA), PP242 (4257, Tocris, Bristol, UK), and Torin1 (4247, R&D Systems, Minneapolis, MN, USA) were used to inhibit mTOR.
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6

Cellular Metabolic Assay Protocol

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Hoechst 33342, valine, concanamycin A (ConA), pepstatin A, reduced glutathione (GSH), paraformaldehyde, mowiol, and trichloroacetic acid (TCA) were all from Sigma-Aldrich, St Louis, MO, USA. Torin1 was purchased from R&D Systems, MN, USA, [ 14 C]valine was from Perkin Elmer, Waltham, MA, USA, and L-leucyl-L-leucine methyl ester (LLOMe) was from Santa Cruz Biotechnology, TX, USA.
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