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11 protocols using poly adp ribose polymerase parp

1

Autophagy and EMT Regulation Pathways

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Chloroquine (CQ), 3-methyladenine (3-MA), rapamycin and TGF- β2 were purchased from Sigma-Aldrich (St Louis, MO, USA). LY2109761 was from Selleck Chemicals (Houston, TX, USA). Antibodies against microtubule-associated protein 1 light chain 3-I (LC3-I), LC3-II, p62, Beclin 1, ATG7, poly (ADP-ribose) polymerase (PARP), cleaved-PARP, caspase 9, cleaved-caspase 9, Bax, and Bcl-x1 were from Abcam (Cambridge, MA, USA). Antibodies against TGF-β2, Smad2, p-Smad2, E-cadherin, α-catenin, β-catenin, N-cadherin, fibronectin, ZO-1, Vimentin, MMP-9, Snail, Slug and β-actin were from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Primary antibodies of LC3-II and E-cadherin and secondary antibodies Alexa Fluor 568 anti-mouse IgG and Alexa Flour 568 anti-rabbit antibodies were from Jackson Immuno Research (Lancaster, PA, USA).
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2

Apoptosis Marker Screening Protocol

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To screen the markers of apoptosis, cells were treated with 15 µM of WTH and 60 µM of CoA and incubated for 1 h, 6 h and 24 h. Cells were thoroughly washed with cold PBS lysed using lysis buffer, composed of radioimmunoprecipitation assay buffer (RIPA) and inhibitors. Protein was quantified using a bovine serum albumin (BSA) assay. An aliquot of 60 mg protein was loaded to wells of sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to nitrocellulose membrane. Membrane was blocked with non-fat dry milk and immunodetected with primary antibodies from Cell signaling technology (CST) (Mabledon Place, London, UK) including poly (ADP-ribose) polymerase (PARP) (CST#9542), Bclxl (CST#2762), caspase-8 (CST#9746), caspase-9 (CST#9501), , caspase-3 (CST#9661) and anti-b-actin (CST#4967), and Bim (ab230531) from Abcam (Cambridge biomedical campus, Cambridge, UK), followed by secondary antibodies. The concentration of each antibody was used according to manufacturer’s protocol.
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3

Cytotoxicity Mechanism of Compound X

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CTD was purchased from Sigma-Aldrich (St. Louis, MO, USA) and high-performance liquid chromatography was used to confirm that the purity was >99%. CTD was dissolved in cell culture medium at a stock concentration of 100 mg/ml and stored at −20°C. The stock solution was freshly diluted in the medium immediately prior to use in each experiment. The primary antibodies for cyclins A and B, CDK1, Bcl-2, Bad and poly ADP ribose polymerase (PARP) were purchased from Abcam Inc. (Cambridge, UK). The p21-specific antibody was obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA) and the antibodies for caspases-3, -7, -8 and -9 and Bid were obtained from Cell Signaling Technology (Beverly, MA, USA). β-actin was purchased from Santa Cruz Biotechnology. Horseradish peroxidase (HRP)-conjugated secondary goat anti-mouse and goat anti-rabbit secondary antibodies were purchased from Pierce. MTS was obtained from Promega (Madison, WI, USA).
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4

Immunoblot Analysis of Apoptosis Markers

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Cells were extracted in a cell lysis buffer (Cell Signaling) with protease inhibitors (Sigma). Proteins were loaded into each lane on a 5–12% gradient sodium dodecyl sulfate/polyacrylamide gel and transferred to immunoblot polyvinylidene fluoride membranes (Bio-Rad). Membranes were blocked with 5% skim milk and probed with primary antibodies at 4°C overnight. Horseradish peroxidase-conjugated secondary antibodies (Beyotime) were applied for 1 h at room temperature. The band intensities were visualized and quantified using an enhanced chemiluminescence detection system (Bio-Rad Laboratories). Primary antibodies used were as follows: poly ADP-ribose polymerase (PARP, 1:1,000, abcam), caspase 3 (1:1,000, abcam), cleaved caspase 3 (1:1,000, abcam), p-JAK1(1:1,000, abcam), p-JAK2 (1:1,000, abcam), and β-actin (1:1,000, Beyotime).
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5

Western Blot Analysis of Apoptosis Markers

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Antibody targeting TXNRD1 (cat. no. ab16840) was purchased from Abcam (Cambridge, UK), and poly (ADP-ribose) polymerase (PARP; cat. no. 9532s), cleaved-PARP (cat. no. 9542) and apoptosis regulator Bax (cat. no. 5023), were from Cell Signaling Technology, Inc. (Danvers, MA, USA). Anti- nuclear factor erythroid 2-related factor 2 (NRF2) antibody (cat. no. sc-81342) was purchased from Santa Cruz Biotechnology (Dallas, TX. USA). Anti-β-actin antibody (cat. no. MABT825) was purchased from Sigma-Aldrich (Merck Millipore). Fluorescence-labeled secondary antibody (IRDye® 800CW; cat. no. 925-32211) was purchased from LI-COR Biosciences (Lincoln, NE, USA). Protein lysates were prepared with radioimmunoprecipitation assay buffer and quantified using the Bradford method with a Bradford Protein Assay kit purchased from Bio-Rad Laboratories, Inc. A total of ~40 µg total protein was used for western blot analysis. Proteins were separated using SDS-PAGE on a 10% gel and subsequently transferred to a polyvinylidene fluoride membrane. Membranes were incubated with primary antibodies at 4°C overnight and with secondary antibodies at room temperature for 2 h. Protein band images were captured using an Odyssey Imaging scanner from LI-COR Biosciences.
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6

Immunofluorescence Analysis of Bladder Tissue

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Collected MPG and PN, and bladder were fixed at 4 °C in 4% paraformaldehyde for 24 hours to make paraffin blocks. The primary antibodies used were as follows: βIII-tubulin (diluted 1:200; Abcam, Cambridge, MA, USA), brain-derived neurotrophic factor (BDNF diluted 1:100; Abcam, Cambridge, MA, USA), poly-ADP-ribose polymerase (PARP, diluted 1:500; Abcam, Cambridge, MA, USA) were used. 6-diamidino-2-phenylindole (DAPI; Vector Laboratories, Inc., Burlingame, CA, USA) was used to stain nuclei. The digital images were obtained by using Zeiss LSM 510 Meta confocal microscope (Zeiss, Oberkochen, Germany). Mean intensity was calculated using ZEN 2012 (Zeiss).
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7

Protein Expression Analysis Protocol

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Protein extraction was performed by using the radioimmunoprecipitation assay buffer supplemented with phosphatase inhibitor cocktails. Equal volumes of protein lysates were separated using 10% (vol/vol) sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred onto polyvinylidene fluoride (PVDF) membranes (Millipore, Billerica, MA, USA). For immunoblotting, antibodies against G protein-coupled receptors 12 (GPR12) (Abcam, USA), poly (ADP-ribose) polymerase (PARP), caspase-3, Cleaved caspase-3, B cell lymphoma-2 (BCL2), BCL-2-Associated X Protein (BAX), phosphorylation of extracellular-regulated protein kinases 1/2 (p-ERK1/2), total extracellular-regulated protein kinases 1/2 (t-ERK1/2) (Cell Signaling Technology Cambridge, MA, USA), α-tubulin, and β-actin (ProteinTech, China) were used.
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8

Immunohistochemical Analysis of Bladder Tissue

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The collected PN and bladder were fixed in 4% paraformaldehyde for 24 h at 4°C
before creating a paraffin block, as described previously9 . The primary antibodies were used as follows: vascular endothelial growth
factor (VEGF; diluted 1:200; Santa Cruz Biotechnologies, Santa Cruz, CA, USA),
βIII-tubulin (diluted 1:200; Abcam, Cambridge, UK), bFGF (diluted 1:500; Cell
Signaling Technology, Danvers, MA, USA), SDF-1 (diluted 1:200; Abcam, Cambridge,
UK), poly-ADP-ribose polymerase (PARP, diluted 1:500; Abcam, Cambridge, UK), and
6-diamidino-2-phenylindole (DAPI; Vector Laboratories, Inc., Burlingame, CA,
USA) were used to stain the nuclei. Digital images were obtained using a Zeiss
LSM 510 Meta confocal microscope (Zeiss, Oberkochen, Germany), and bladder
images were analyzed using ZEN 2012 (Zeiss, Oberkochen, Germany). The other
resulting images were analyzed using Image J to determine the positive rate for
each figure. In brief, we used Image J to split each color from merged figure,
calculate the intensity of each color, and then added them. The positive was the
ratio of a special color fluorescence intensity to all colors intensity.
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9

Apoptosis Induction in Gastric Cancer

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F12, RPMI‐1640 medium and foetal bovine serum (FBS) were purchased from Gibco, BRL (Grand Island, NY, USA). PGE2 ELISA kit ADI‐900‐001 was purchased from Enzolifesciences (Farmingdale, NY, USA). Hoechst 33258 was purchased from Sigma‐Aldrich (St Louis, MO, USA). The Annexin V‐FITC Apoptosis Kit was purchased from Becton Dickinson (Franklin Lakes, NJ, USA). Mitochondrial Membrane Potential Assay Kit was purchased from Beyotime Biotechnology (Jiangsu, China). The primary antibodies against ATF‐4, Chop, Bax, Bcl‐2, Mcl‐1, Puma, Noxa, Bim, Bak, procaspase‐3, active caspase‐3, procaspase‐9, poly ADP‐ribose polymerase (PARP) and β‐actin were purchased from Abcam Inc. (Cambridge, MA, USA). Human gastric carcinoma cell line AGS and HGC‐27 cells were purchased from Shanghai Institutes for Biological Sciences, CAS (Shanghai, China). Cells were cultured with F12 or RPMI 1640 medium containing 10% FBS and 1% penicillin/streptomycin at 37°C, 5% CO2 humidified atmosphere. Both ABT‐737 and DMC were dissolved in Dimethyl sulfoxide (DMSO) at the concentration of 100 mM.
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10

Propofol-induced Apoptosis Assay

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Propofol (Fresenius Kabi Austria Gmbh, Hafnerstrasse, Austria) diluted with dimethyl sulfoxide (DMSO), Hoechst 33342, and chloroquine were purchased from Sigma (St. Louis, MO, USA). The following reagents were obtained commercially: 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide (MTT), acridine orange (AO), monodansylcadaverine (MDC), and 3-methyladenine (3-MA, class III PI3K inhibitor) (Calbiochem, La Jolla, CA, USA). The antibodies used in the study were as follows: Bak (1:1000), caspase-9 (1:1000), caspase-3 (1:1000), and poly (ADP-ribose) polymerase (PARP; 1:1,000) (Abcam, Cambridge, MA, USA).
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