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80 protocols using torin1

1

Cell Culture Protocol for RPE and C2C12

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RPE, also known as ARPE-19, and immortalized mouse myoblast cell line, C2C12, were obtained from ATCC (Manassas, VA, USA). RPE cells were maintained in either MEM or high-glucose DMEM, both media without sodium pyruvate, plus 10% FBS and C2C12 cells were cultured in high-glucose DMEM without pyruvate plus 10% FBS. Serum-free low-glucose DMEM was used in some experiments. Rapamycin was obtained from LC Laboratories (Woburn, MA, USA). Torin 1 was purchased from Selleckchem (Houston, TX, USA). Insulin (as 10 mg/ml solution) and PF 4708671 were obtained from Sigma-Aldrich (St. Louis, MO, USA). Stock solutions were prepared in DMSO: Rapamycin at 5 mM and 50 μM; Torin 1 at 3 mM; PF4708671 at 10 mM.
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2

Elaiophylin Biosynthesis from Deep-Sea Streptomyces

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Elaiophylin was prepared from the deep-sea-derived Streptomyces sp. SCSIO 1934 [44 (link)]. Rapamycin, torin1, bafilomycin A1, compound C, STO-609, and rosiglitazone were purchased from Selleck. Insulin, IBMX, and dexamethasone were purchased from Sigma-Aldrich. Antibodies recognizing phospho-AMPKα (#2535), AMPKα (# 2532), phospho-ACC (#3661), ACC (#3662), phospho-AKT (#4060), phospho-S6K (#9204), S6K (#9202), 4EBP1 (#9644), phospho-ERK (#4370), phospho-c-JUN (#3270), and LC3B (#3868) were procured from Cell Signaling. Other antibodies included anti-AKT (Proteintech, 60203-2-Ig), anti-GST (Proteintech, 10000-0-AP), anti-TXNIP (Abcam, ab188865), and anti-ACTIN (Genescript, A00702).
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3

Mitochondrial Dynamics Regulation

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SP600125, SB203580, and N-acetyl cysteine (NAC) were obtained from Sigma-Aldrich. Torin1 and Mdivi-1 were purchased from Selleck. Antibodies against mitofusin (MFN)-1, mitofusin (MFN)-2, PARP, caspase3, p62, and β-actin were obtained from Proteintech. Antibodies against dynamin-related protein (Drp)-1 were obtained from ABclonal. Antibodies against cleaved caspase-3, cleaved PARP, and LC3 were obtained from Cell Signaling Technology.
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4

Compound Screening for Drug Discovery

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Chemicals used in this study were from the following sources: nilotinib (Selleckchem, S1033), imatinib (Selleckchem, S2475), torin1 (Selleckchem, S2827), Gefitinib (MedChemExpress, HY-50895), GSK621 (Sigma, SML2003), EX229 (MedChemExpress, HY-112769), BC1618 (MedChemExpress, HY-134656), bafilomycin A1 (Selleckchem, S1413), MK2206 (Selleckchem, S1078), SRT1720 (Apexbio, A4180–10), FR180204 (Selleckchem, S7524), PLX-4720 (Selleckchem, S1152). PEG300 (Selleckchem, S6704), DMSO (Sigma, D2650).
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5

Investigating mTOR Inhibition in Glioma

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mTOR inhibitor Torin1 (Tocris Biosciences) was resuspended in DMSO and used at final concentrations of 0.5 μM for short term 1–2 Hr treatments in C6 cells or rat cortical neurons (DIV13) for 6 Hr at 37°C. Bafilomycin A1 (Selleck Chemicals, #S 1413) was resuspended in DMSO and used at final concentration of 100nm for 2–6 Hr in combination with Torin1 in C6 glioma cells.
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6

Engineered Hypoxia Response Pathway

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pLenti-EglN1 mammalian expression plasmid, HIF-responsive element (HRE)-containing plasmid and lentiviral shRNA constructs targeting human EglN1, EglN2 and EglN3 were obtained from Dr. William G. Kaelin, Jr (Dana Farber Cancer Institute, Boston). Site-directed mutagenesis was performed to generate various EglN1 mutants using the QuikChange XL Site-Directed Mutagenesis Kit (Stratagene, City) according to the manufacturer’s instructions. SH-HIF1a and SHI-HIF2a lenti plasmids were gifts from Dr. M. Celeste Simon (Perelman School of Medicine, University of Pennsylvania). pCDNA3-HIF1a was constructed by Dr. Frank Lee. Deoxy-2-[(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]-d-glucose (catalog number 72987) was purchased from Sigma and Torin1 (catalog number S2827) from Selleckchem.
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Cellular Signaling Pathway Analysis

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Torin1 (Selleck Chemicals, S2827), bafilomycin A1 (Selleck Chemicals, S1413), chloroquine (Sigma, C6628), EGF (PeproTech incorporated, AF-100–15), nocodazole (Sigma, M1404), puromycin (Sigma, P7255), Lipofectamine 3000 (Thermo Fisher Scientific, L3000015), Earle’s basic salt solution (Thermo Fisher Scientific, 1816327), restriction enzymes (Thermo Fisher Scientific), GST agarose (Probegene, PC014), 2× Taq Master Mix (Probegene, ME013), 2 × Ultra-Pfu Master Mix (Probegene, ME026), ClonExpress II One Step Cloning Kit (Vazyme Biotech, C112-01), 2 × Phanta Master Mix (Vazyme Biotech, P511).
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8

Molecular Mechanisms of Cellular Stress Response

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Celastrol, cycloheximide (CHX), 3-methyladenine (3-MA), bafilomycin A1, chloroquine (CQ), ethylene glycol tetraacetic acid (EGTA), 1,2-bis(o-aminophenoxy) ethane-N,N,N'N'-tetraacetic acid (BAPTA), 1,2-bis(o-aminophenoxy)ethane-N,N,N'N'-tetraacetic acid acetoxymethyl ester (BAPTA-AM), ruthenium red, and MG132 were purchased from Sigma-Aldrich. Torin1 was purchased from Selleckchem. LysoTracker-Red, Rhod-2-AM, Fluo-3-AM, calcein- acetoxymethyl ester (calcein-AM), and ethidium homodimer-1 (EthD-1) were from Molecular Probes. 2-aminoethosxydiphenyl borate (2-APB), PD98059, SB203580, and SP600125 were obtained from Calbiochem. Dantrolene was obtained from Alexis Biochemicals. The following antibodies were used: anti-β-actin (Abcam); anti-ubiquitin, ATF4, and IP3R (Santa Cruz Biotechnologies); anti-caspase-8, caspase-3, and KDEL (Stressgen); anti-caspase-9 (Novus Biologicals); anti-p62 and anti-cathepsin L (BD Biosciences); anti-MCU (Sigma-Aldrich); anti-NBR1 (Abnova); anti-LC3B, CHOP, phospho-ERK1/2, total ERK1/2, phospho-JNK, total JNK, phospho-p38, and total p38 (Cell Signaling); HRP-conjugated anti-rabbit IgG and HRP-conjugated anti-mouse IgG (Molecular Probes).
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9

Pharmacological Modulation of Cellular Pathways

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Rapamycin was from Calbiochem (#53123-88-9). Torin1 (#S2827), BI-D1870 (#S2843), CKI-7 (#S2248), GSK-429286A (#S1474), GSK-650394 (#S7209) were from SelleckChem. Forskolin (#1099), 3-isobutyl-1-methylxanthine (IBMX, #2845) and H89 (#2910) were from Tocris. Insulin (#I1507) and calyculin A (#101932-71-2) were from Sigma. Okadaic acid (#O-5857) was from LC Laboratories.
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10

Inducible p21 Expression in HT-p21 Cells

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HT-p21 cells, derived from HT1080 human fibrosarcoma cells, in which p21 expression can be turned on and off using IPTG (isopropyl-thio-galactosidase) were described [80 (link), 81 (link), 62 (link)]. HT-p21 cells were cultured in DMEM/10% FC2 serum (HyClone FetaClone II; HyClone Laboratories, Inc, Logan, UT), Immortalized WI38t human fibroblasts, described previously [111 (link)], and SKBR3, breast adenocarcinoma cell line (ATCC, Manassas, VA), were maintained in DMEM/10% FBS. Rapamycin was purchase from LC Laboratories (Woburn, MA). Torin 1 and PP242 were from Selleckchem (Houston, TX). Stock solutions were prepared in DMSO.
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