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15 protocols using anti bim

1

RIPK1-Mediated Necroptosis Signaling

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Stimulated T cells were incubated in lysis buffer. For signaling complex analyses, cell lysates were pre-cleared with Protein G beads prior to immunoprecipitation with anti-RIPK1 antibody. Antibodies and reagents used for immunoprecipitation and immunoblotting studies included: anti-RIPK1, anti-Bim, anti-Bclx, (BD Biosciences), nec1, anti-Bcl2, β-actin (Merck chemicals), anti-RIPK3 (ProSci Incorporated), anti-ubiquitin, anti-Bax, anti-RIPK3 (Santa Cruz Biotechnology), anti-RIPK1, anti-A20 (Cell signaling Technology), QVD, ZVAD (Enzo Life Science).
Signaling studies in MEFs were performed as described19 (link). RIPK1 immunoprecipitations were performed using anti-RIPK1 (Cell Signaling) and Dynabeads M270 Epoxy (Invitrogen). K63-ubiquitin immunoprecipitations were performed using anti-K63 (Millipore) and Dynabead Protein A (Invitrogen). Studies of RIPK3 mutants in A20−/−Ripk3−/− MEFs were performed by generating RIPK3 lysine mutants, introducing mutant RIPK3-encoding cDNAs into GFP expressing lentiviral constructs, and infecting A20−/−Ripk3−/− MEFs with these viruses. Productively infected cells were FACS-sorted to obtain pure populations of RIPK3-expressing cells prior to being tested in necroptosis assays. Cell survival of MEFs was quantitated using the CellTiter-Glo Luminescent Cell Viability Assay per manufacturer’s instructions (Promega).
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2

Cellular Signaling Pathway Characterization

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Dulbecco’s Modified Eagle’s Medium (DMEM), Fetal Bovine Serum (FBS), and Penicillin/Streptomycin were procured from GIBCO-BRL (USA). Antibodies against PI3K, p-PI3K, Akt, p-Akt (Ser473), cleaved caspase-3, Bax, Bcl-2, p-Fox03A (Thr32), Fox03A, and β-actin were purchased from Cell Signaling Technology (USA) and anti-BIM was purchased from BD Bioscience.
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3

Apoptosis and Oxidative Stress Assay

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Bicinchoninic acid (BCA), trichloroacetic acid (TCA), sulforhodamine B (SRB), propidium iodide, RNase A, dimethyl sulfoxide (DMSO) and catalase were purchased from Sigma-Aldrich, Inc. (St. Louis, MO, USA). Roswell Park Memorial Institute (RPMI) 1640 medium, Dulbecco Modified Eagle Medium (DMEM)/high glucose, Minimum Essential Media (MEM), fetal bovine serum (FBS), trypsin-EDTA solution (1X), antibiotic-antimycotic solution (100X), and PBS (1X) were purchased from HyClone Laboratories, Inc. (South Logan, UT, USA). Anti-caspase-9, anti-cleaved caspase-9, anti-caspase-3, anti-BID, anti-p-p53 (Ser15), anti-Prx1, anti-caspase-8, and anti-cleaved caspase-8 were purchased from Cell Signaling Technology (Danvers, MA, USA). Anti-cleaved caspase-3, anti-Bax, anti-Bcl-2, anti-p53, anti-catalase, anti-SOD-1, anti-SOD-2, anti-GPx-1, anti-Trx, anti-PrxI/II, anti-β-actin, and all secondary antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Anti-BIM, anti-PARP, anti-cleaved PARP, and fluorescein isothiocyanate (FITC) Annexin V apoptosis detection kit I were purchased from BD Biosciences (CA, USA). Anti-RIP-3 was purchased from Abcam (Cambridge, MA, USA). 2′,7′-dichlorodihydrofluorescein diacetate (DCFH2-DA) was purchased from Invitrogen (Carlsbad, CA, USA).
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4

Cellular Stress Response Assay Reagents

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N-acetyl cysteine, CuDIPS and polyethylene glycol catalase, CHX, 3-methyladenine (3-MA), bafilomycin A1, CQ, 4′,6-diamidino-2-phenylindole and crystal violet were purchased from Sigma-Aldrich (St. Louis, MO, USA). MitoSOX-Red, calcein acetoxymethyl ester (calcein-AM) and ethidium homodimer (EthD-1) were purchased from Molecular Probes (Carlsbad, CA, USA). MnTBAP, PD98059, U0126 and SB203580 were obtained from Calbiochem (San Diego, CA, USA). L-JNKI was purchased from Enzo Life Sciences, Inc. (Farmingdale, NY, USA). The following antibodies were used: monoclonal anti-β-actin (Sigma-Aldrich); anti-ubiquitin, ATG6 (BENC1) and ATF4 (Santa Cruz Biotechnologies, Santa Cruz, CA, USA); anti-KDEL (Stressgen, Ann Arbor, MI, USA); anti-Noxa and anti-Bim (BD Biosciences Pharmingen, San Jose, CA, USA); anti-phospho-ERK1/2, total ERK1/2, phospho-JNK, total JNK, ATG5, CHOP (GADD153), LC3B, and AIP-1/Alix (Cell Signaling, Beverly, MA, USA); horseradish peroxidase (HRP)-conjugated anti-rabbit IgG and HRP-conjugated anti-mouse IgG (Molecular Probes).
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5

Investigating Cancer Cell Signaling Pathways

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Human renal carcinoma (Caki-1 and A498), human lung cancer (A549), and human breast cancer (MDA-MB361) were procured from American Type Culture Collection (Manassas, VA, USA). Human recombinant TRAIL, zVAD-fmk, and anti-survivin were provided by the R&D system (Minneapolis, MN, USA). MG132, PD98059, AG-490, compound C, and NVP-BEZ235 were supplied from Calbiochem (San Diego, CA, USA). Dexamethasone, cycloheximide, AR-A014418, PP242, BAY11-7082, rapamycin, and anti-actin were provided from Sigma Chemical Co. (St. Louis, MO, USA). Anti-PARP, anti-Bcl-xL, anti-DR5, anti-cIAP1, anti-caspase-8, anti-phospho-GSK3β, and anti-GSK3β were provided by Cell Signaling Technology (Beverly, MA, USA). Anti-Bim, anti-Bax, and anti-XIAP were obtained from BD Biosciences (San Jose, CA, USA). Anti-Mcl-1, anti-Bcl-2, anti-cIAP2, and anti-Cbl were purchased from Santa Cruz Biotechnology (St. Louis, MO, USA). SB203580, SP600125, and anti-c-FLIP(L) were obtained from Enzo Life Sciences (San Diego, CA, USA). Anti-DR4 were obtained from Abcam (Cambridge, MA, USA). pCMV-Myc-Cbl plasmid was a gift from Dr. S. J. Kim (CHA University, Korea). GSK3betaS9A (1016) was a gift from Scott Friedman (Addgene plasmid # 49492; http://n2t.net/addgene:49492; RRID: Addgene_49492) [36 (link)].
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6

Viral Interactome Profiling by Co-Immunoprecipitation

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Cells were infected with various viruses and cells were lysed at 24 hr post-infection and protein complexes were isolated using anti-Flag Ab coated agarose beads. The proteins bound to the beads were washed 4 times and suspended in 40 μl sample buffer. The lysates and immunoprecipitated samples were separated by 4-12 % gradient gels, transferred to nitrocellulose membrane and incubated at 4°C overnight with the following antibodies; anti-Flag (Sigma), anti-BIK, anti-prohibitin 1 and 2 and anti-actin (Santa Cruz), anti-DNA-PKcs and anti-ATP synthase (Protein Tech), anti-BAK and anti-BAX (Upstate), anti-BIM, anti-BID and anti-PARP (BD Pharmingen). The blots were washed and incubated with the corresponding secondary antibodies conjugated with HRP (Santa Cruz) for 30 min. The blots were then washed and the protein bands were visualized with western blotting detection system (Roche) according to the manufacturer's specifications. The quantitation of cleaved PARP was carried out using BIO-RAD CHEMI DOC XRS system by measuring the relative intensities of the cleaved products.
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7

Molecular Mechanisms of TRAIL-Induced Apoptosis in Cancer Cells

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Selleckchem supplied R428 and cisplatin (Houston, TX, USA), and R&D system supplied recombinant human recombinant TRAIL and z-VAD-fmk (Minneapolis, MN, USA). Sigma Chemical Co. provided MG132, cycloheximide, carboplatin, oxaliplatin, doxorubicin, and 5-FU (St. Louis, MO, USA). The primary antibodies were as follows: Anti-phospho-Axl (Y702) (Cell Signaling Technology, Beverly, MA, USA), anti-pro-caspase-3 (Cell Signaling Technology), anti-cleaved caspase-3 (Cell Signaling Technology), anti-PARP (Cell Signaling Technology), anti-Bcl-xL (Cell Signaling Technology), anti-DR5 (Cell Signaling Technology), anti-actin (Sigma Chemical Co.), anti-Axl (Santa Cruz Biotechnology, St. Louis, MO, USA), anti-Mcl-1 (Santa Cruz Biotechnology), anti-Bcl-2 (Santa Cruz Biotechnology), anti-cIAP2 (Santa Cruz Biotechnology), anti-Bim (BD Biosciences, San Jose, CA, USA), anti-XIAP (BD Biosciences), anti-survivin (R&D system, Minneapolis, MN, USA), anti-DR4 (Abcam, Cambridge, MA, USA), and anti-c-FLIP (Enzo Life Sciences, San Diego, CA, USA). The siRNAs were as follows: GFP (control) siRNA (Bioneer, Daejeon, Korea), Axl siRNA (Santa Cruz Biotechnology), and DR5 siRNA (Invitrogen).
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8

Hispolon sensitizes TRAIL-induced apoptosis

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American Type Culture Collection (Manassas, VA, USA) supplied the all cells and the transformed mouse kidney cells (TCMK-1) was a gift from Dr. TJ Lee (Yeungnam University, Korea). The cells were cultured using Dulbecco’s modified Eagle’s medium containing 10% FBS, 20 mM HEPES buffer and 100 μg/mL gentamycin. Hispolon was purchased from ENZO life Science (Farmingdale, NY, USA). The recombinant human TRAIL was purchased from KOMA Biotech (Seoul, Korea). Anti-DR5 (1:700, #8074), Bcl-xL (1:700, #2764), and anti-PARP (1:700, #9542) antibodies were purchased from Cell Signaling Technology (Beverly, MA, USA). Anti-DR4 (1:1,000, ab8414), and anti-cIAP1 (1:700, ab154525), antibodies were purchased from Abcam (Cambridge, UK). Anti-c-FLIP (1:700, ALX-804-961-0100) antibody was obtained from Enzo Life Sciences. Anti-Mcl-1 (1:700, sc-819) and anti-cIAP2 (1:700, sc7944) antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Anti-XIAP (1:1,000, 610762) antibody and anti-Bim (1:700, AB17003) antibodies were purchased from BD Biosciences (San Jose, CA, USA). Cyclohexamide and other reagents were purchased from Sigma Chemical Co. (St. Louis, MO, USA).
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9

Apoptosis Induction Reagents Protocol

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Sigma Chemical Co. provided magnolol, cycloheximide, bafilomycin A1, leupeptin and anti-actin (St. Louis, MO, USA). R&D Systems supplied recombinant human TRAIL and z-VAD (Minneapolis, MN, USA). Enzo Life Sciences provided lactacystin, anti-pro-caspase-3 and anti-c-FLIP (Ann Arbor, MI, USA). Santa Cruz Biotechnology provided anti-Mcl-1, anti-Bcl-2, anti-cIAP2 and anti-ATF4 (St. Louis, MO, USA). Cell Signaling Technology supplied anti-PARP, anti-cleaved caspase-3, anti-Bcl-xL, anti-DR5 and anti-CHOP (Beverly, MA, USA). BD Biosciences provided anti-Bim and anti-XIAP (San Jose, CA, USA).
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10

Apoptosis Induction in Cancer Cells

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Human renal carcinoma (Caki, ACHN, and A498), human breast carcinoma cells (MCF-7), human lung carcinoma cells (A549), normal human umbilical vein cell (EA.hy926), and normal mouse kidney cells (TCMK-1) were obtained from the American Type Culture Collection (Manassas, VA, USA). All cells were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum, 20 mM HEPES buffer, 100 U/ml penicillin, 100 μg/ml streptomycin, and 100 μg/ml gentamicin. The PCR primers were purchased from Macrogen (Seoul, Korea). Recombinant human TRAIL and BIX were purchased from Sigma Chemical Co. (St. Louis, MO, USA). z-VAD-fmk and anti-survivin antibodies were purchased from R&D system (Minneapolis, MN, USA). Anti-Mcl-1 and anti-cIAP2 antibodies were purchased from Santa Cruz Biotechnology (Dallas, TX, USA). Anti-Bim and anti-XIAP antibodies were purchased from BD Biosciences (San Jose, CA, USA). Anti-PARP, anti-Bcl-2, anti-Bcl-xL, anti-DR5, and anti-G9a antibodies were purchased from Cell Signaling Technology (Beverly, MA, USA). Anti-actin antibody and other chemicals were purchased from Sigma Chemical Co.
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