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5 protocols using poly mono adp ribose

1

Protein Regulation and Stress Response

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All reagents were obtained from commercial sources; CTX, sodium tetrasulfide (Na2S4), N-acetylcysteine, 2′,7′-dichlorodihydrofluorescein diacetate (WAKO), rucaparib, KRIBB11 (Selleck), I3MT-3 (MedChemExpress), PAG (Sigma-Aldrich). The antibodies used were against FLAG (Sigma), p62 (MBL), AIF, K48-linked ubiquitin, poly/mono-ADP Ribose (Cell Signaling Technology), β-actin, PARP-1, Lamin A/C, HSP70, HSF1 (Santa cruz). Complementary DNAs (cDNAs) encoding human HSP90AB1 was obtained by performing PCR and was inserted into pcDNA3 with FLAG tag plasmid as described previously (49 (link)). Plasmid transfection was performed using PEI “Max” (Polysciences), according to the manufacturer’s instructions. siRNA targeting human HSP70 was obtained from GeneDesign (50 (link)). HT1080 cells were transfected with 10 nM nontargeting siRNA pool (Dharmacon) as control or HSP70 siRNAs using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen), according to the manufacturer’s instructions. HSP70 siRNA sequences were 5′- CACGGCAAGGUGGAGAUCA′ (HSP70 #1) and 5′- UGCACCUUGGGCUUGUCUCCGUCGU′ (HSP70 #2).
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2

Western Blot Analysis of Cardiac Markers

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The heart tissue and H9C2 cells were ground and lysed by protein lysis buffer (Beyotime, China) with PMSF and phosphatase inhibitor cocktail. Total protein samples were extracted from the lysate, and the protein concentration was detected. The sample was loaded into 8% or 12% SDS-PAGE gel for electrophoresis and then transferred to the PVDF membrane. It was blocked for 1 hour and then immersed in primary antibody for 12 hours at 4°C, such as GAPDH (Proteintech, 60004-1-Ig, USA), GSDMD (Abcam, ab219800, ab209845, UK), NLRP3 (Abcam, ab214185, UK), caspase-1 (Abcam, ab179515, UK), IL-1β (Abcam, ab9722, UK), caspase-3 (Cell Signaling Technology, 14220T, USA), caspase-7 (Cell Signaling Technology, 12827T), caspase-8 (Beyotime, AC056, China), Bcl-2 (Beyotime, AB112, China), Bax (Beyotime, AB026, China), PARP-1 (Cell Signaling Technology, 9532S, USA), and poly/mono-ADP ribose (Cell Signaling Technology, 83732S, USA). The membranes were washed with TBST twice, immersed in the secondary antibody for 1 hour, and then washed again. Bands were displayed by the ECL detection kit (Millipore, USA).
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3

Quantifying PAR Induction by PARPi and H2O2

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Cells were seeded into 384-well plates (Greiner, Austria; 781090) using a Multidrop Combi (Thermo Fisher Scientific) and incubated overnight at 37°C and 5% CO2 in a rotating incubator. PARPi compounds were added with Echo555 (LabCyte), with final compound concentration range between 1.6 pmol/L and 30 μmol/L. After 1 hour incubation with PARPi, H2O2 was added at final concentration of 10 mmol/L and incubated for 5 min in culture conditions. Cells were then fixed in ice-cold methanol for 15 minutes at 4°C and processed for immunostaining with primary antibody Poly/Mono-ADP Ribose (Cell Signaling Technology, #83732) followed by secondary goat anti-rabbit AlexaFluor-488 antibody (Invitrogen, #A-11008); nuclei were counterstained with DAPI. The nuclear PAR fluorescence intensity (F.I.) was acquired and analyzed using CellInsight CX5 HCS Platform (Thermo Fisher Scientific); dose–response curves were generated with GraphPad Prism software.
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4

Comprehensive Immunoblotting Protocol

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For immunoblotting, proteins were resolved on SDS-PAGE and analyzed using the LI-COR Odyssey Imager (LI-COR). The following primary antibodies were used (Appendix Table S3): ATG3 (A3231), MAP1LC3A (LC3, L8918), TUBA4A (alpha-Tubulin, T5168) from Sigma-Aldrich; ACTB (beta-Actin, 3700), SQSTM1 (p62, 5114), ATG7 (8858), Acetylated-Lysine (9441), FOXO1 (2880), GAPDH (2118), RELA S536 (NF-κB p65 S536, 3036), RELA (NF-κB p65, 6956), MTOR (2971), MTOR S2448 (4517), AMPKα T172 (2531), AMPKα (2793), P70S6K T389 (9206), P70S6K (2708), ULK1 (8054), Sirtuin antibody sampler kit (9787), SIRT4 (69786), PARP1 (9532), GFP (55494), Poly/Mono-ADP Ribose (83732), and PRKN (Parkin, 4211) from Cell Signaling Technology; Ac-FKHR (D-19, sc-49437), PPARGC1A (PGC1α, H-300, sc-13067), GAPDH (SC-32233), SIRT1 (B-10, sc-74504), and TOMM20 (TOM20, sc-17764) antibodies from Santa Cruz Biotechnology (Santa Cruz Biotechnology, Dallas, TX); CD38 (60006-1-lg), BST1 (CD157, 16337-1-AP), NMNAT1 (11399-1-AP), NMNAT3 (13261-1-AP), PARP2 (2055-1-AP), and NNMT antibody (15123-1-AP) and PINK1 antibody (23274-1-AP) from Proteintech (Rosemont, IL); NMNAT2 (PA5-115662) from Invitrogen (ThermoFisher Scientific); SDHA (ab14715) antibody from Abcam.
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5

Protein Extraction and Western Blot Analysis

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All chemicals were purchased from Sigma unless otherwise noted. Cells were lysed in RIPA buffer (20 mM Tris, pH 7.4, 150 mM NaCl, 1% NP-40, 10% glycerol, 1 mM EDTA, 1 mM EGTA, 5 mM NaPPi, 50 mM NaF, 10 mM Na β-glycerophosphate) plus fresh HALT protease inhibitor cocktail (Pierce) and 1 mM Na3VO4 (New England Biolabs). Frozen tumor fragments were thawed, homogenized, and lysed in the same solution. Cell/tumor lysates were sonicated at 30% power for 15 s, centrifuged at 17,000 x g for 10 min at 4°C, and protein content in supernatant was quantified by BCA Assay (Pierce). Protein extracts were reduced and denatured in LDS sample buffer (GenScript) plus 1.25% β-mercaptoethanol. Proteins were separated by SDS-PAGE, transferred to nitrocellulose, and stained with Ponceau S to visually confirm protein loading and transfer. Blots were probed with primary antibodies against ER (Santa Cruz Biotechnology; cat.# sc-8002), vinculin (Cell Signaling Technology; cat.# 13901), PR (Cell Signaling Technology; cat.#8757), poly/mono-ADP ribose (Cell Signaling Technology; cat.#83732), Rb (Cell Signaling Technology; cat.#9309), phospho-RbS780 (Cell Signaling Technology; cat.#9307), and FLAG (Millipore Sigma; cat.# F3165). Signal was detected with DyLight conjugated secondary antibodies (Cell Signaling Technology) using the LI-COR Odyssey system (LI-COR Biosciences).
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