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14 protocols using ac p53

1

Molecular Mechanisms of DMF in Cellular Stress

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Hydrogen peroxide (H2O2, #MKBK8393V) and paraformaldehyde solution (#SZBC2290V) were purchased from Sigma-Aldrich. 5-Bromo-4-chloro-3-indolyl-β-D-galactosidase (X-gal, 11680293001) was purchased from Roche. Antibodies against the following proteins were used: DRG2 (Proteintech group, 14743-1-AP), acetyl-p53 (ac-p53, Cell Signaling Technology (CST), #2525), p53 (CST, #2524), p21Waf1/Cip1 (Santa Cruz Biotechnology (SCBT), sc-397), cyclin D1 (SCBT, sc-717), p16INK4α (BD Pharmingen, 551163), SIRT1 (Merck Millipore, 07-131), SIRT1 (Abcam, ab110304), acetyl-NF-κB p65 (ac-NF-κB p65, CST, #3045), NF-κB p65 (SCBT, sc-8008), phosho-Histone H2A.X (p-H2A.X, CST, 9718 s), and β-actin (SCBT, sc-1616). Secondary antibodies for immunoblotting were from SCBT (goat anti-mouse IgG-HRP, sc-2005; mouse anti-rabbit IgG-HRP, sc-2357; donkey anti-goat IgG-HRP, sc-2020), and those for immunofluorescent staining were from Invitrogen (goat anti-rabbit Alexa Fluor 568, A-11011; goat anti-mouse Alexa Fluor 488, A-11001; goat anti-mouse Alexa Fluor 568, A-11004). DMF (6,4′-dihydroxy-7-methoxyflavanone) was obtained from the Standardized Material Bank for New Botanical Drugs (no. NNMBP012), Wonkwang University (Republic of Korea). DMF (>98%) was isolated from the heartwood of Dalbergia odorifera [25 (link)] and was dissolved in DMSO (0.05% in final culture concentration).
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2

Western Blot Analysis of Protein Expression

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After washing, cold RIPA with protease inhibitors (Roche) was used to lyse cells for 15 min. Then, after centrifugation, the cell supernatant was kept frozen at −80°C until use. Bradford assays (Bio-Rad Laboratories; CA, USA) were employed to assess protein concentrations. Samples (20 μg) were separated via SDS-PAGE, after which dry transfer to nitrocellulose membranes was conducted. After being blocked in 5% BSA for 1 h, primary antibodies were used to probe the membranes overnight at 4°C, including antibodies targeting human SIRT1, acetylated-p53 at K382 (Ac-p53), p21, forkhead box O1 (FoxO-1) (Cell Signaling Technology; USA), Ac-FoxO-1, total p53 (1: 2000 dilution), and senescence marker protein-30 (SMP-30) (all from Santa Cruz Biotechnology). β-actin served as an internal control and was purchased from Sigma Aldrich. After incubation with the appropriate secondary antibodies (1: 10 000 dilution; GE Healthcare, Buckinghamshire, UK), the immunostained protein bands were visualized with an ECL system (ProteinSimple; Santa Clara, USA), followed by quantification using ProteinSimple image software. All samples had 3 biological replicates, and each biological replicate was assayed in duplicate; therefore, the data for each time point are an average of 6 individual replicate runs. Representative images of the immunostained bands are presented in the figures.
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3

Quantitative Protein Analysis Protocol

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Whole cell lysates were collected using RIPA buffer with added protease inhibitor cocktail (Roche). Insoluble fractions were collected using Urea-containing buffer. Protein was quantified using Bradford assay reagent (Biorad) and bovine serum albumin standards (Pierce). Equal amounts of protein were electrophoresed in SDS-PAGE gels and transferred to PVDF membrane Immobilon-FL (Millipore). Blots were developed using ECL-plus (GE) for 5 minutes, chemiluminescence visualized on a Licor Odyssey FL imager and quantitation done using Licor Image Studio software. All quantitated protein signals were normalized to GAPDH signal from the same gel. Antibodies used were as follows: SIRT1 (Cell Signaling), SIRT2 (Abcam), SIRT3 (Sigma), Involucrin (Santa Cruz), Cytokeratin 10(Santa Cruz), GAPDH (Santa Cruz), p-NBS1 Ser 343 (Cell Signaling), NBS1 (Santa Cruz), ac-p53 (Cell Signaling), p53 (Calbiochem), pATM Ser 1981 (Cell Signaling), ATM(Cell Signaling), pCHK2 Ser 19 (Cell Signaling), CHK2(Cell Signaling).
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4

Evaluating Protein Levels in Brain

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Protein levels of ac-NF-кB, ac-FoxO1, SIRT1, and ac-p53 in brain samples were evaluated by western blotting according to standard protocols. In brief, the protein samples were blotted onto the PVDF membrane. Then, the membrane was incubated with primary antibodies against SIRT1 (Ab12193, 1 : 1000, Abcam), ac-FoxO1 (sc-49437, 1 : 200, Santa Cruz), ac-NF-кB (12629S, 1 : 500, Cell Signaling), ac-p53 (2570, 1 : 500, Cell Signaling), and appropriate secondary antibodies. β-Actin (BM0627, 1 : 4000, Boster Biotech) was the internal loading control for the proteins. Membranes were observed with enhanced chemiluminescence solution.
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5

Protein Expression Analysis in mGSCs

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Total cell extracts were prepared from mGSCs cells, and proteins were extracted in 1×SDS–PAGE sample loading buffer. Total cell proteins were resolved by SDS–PAGE, transferred to PVDF membrane, and probed with β-Actin (1:1000, Beyotime), SIRT1 (1:1000, Cell Signaling Technology), P53 (1:1000; Cell Signaling Technology), Ac-P53 (1:1000; Cell Signaling Technology), Horse-radish peroxidase conjugated anti-rabbit IgG was used as a secondary antibody (1:1000, Beyotime). The detection was performed using the BM-Chemiluminescence blotting substrate (Roche, Shanghai, China), then the maps have been analyzed by ImageJ (V1.48d) for their integrated density [42 (link)].
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6

Protein Extraction and Western Blot Analysis

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Whole cell protein extraction, cytosolic protein extraction, and nuclear protein extraction were carried out according to established protocols [44 (link),45 (link)]. Equal protein amounts were separated by polyacrylamide gel electrophoresis and transferred to a polyvinylidene difluoride membrane. The membrane was blocked in 5% skim milk for 2 h at room temperature and then incubated with primary antibodies against Bcl2 (1:200, Santa Cruz, Dallas, TX, USA), Bax (1:200, cat# sc-493, Santa Cruz), caspase-3 (1:400, cat# 9661, Cell Signaling), Nrf2 (1:1000, cat# ab31163, Abcam), HO-1 (1:1000, cat# ab13243, Abcam), NQO-1 (1:1000, cat# ab34173, Abcam), SIRT1 (1:200, cat# SC-15404, Santa Cruz), ac-FoxO1 (1:200, cat# sc-49437, Santa Cruz), ac-p53 (1:400, cat# 2570, Cell Signaling), β-actin (1:3000, cat# AP0060, Bioworld Technology, Minneapolis, MN, USA), and Histone H3 (1:3000, cat# BS7416, Bioworld Technology) overnight at 4 °C. Subsequently, the membrane was incubated with horseradish peroxidase (HRP)-conjugated IgG for 2 h at room temperature. Protein bands were detected by enhanced chemiluminescence solution (Thermo Fisher Scientific, Waltham, MA, USA). Band density was quantified with UN-Scan-It 6.1 software (Silk Scientific Inc., Orem, UT, USA).
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7

Western Blot Analysis of Cellular Proteins

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Heart tissue or NRCMs were lysed in RIPA buffer containing 20 mM Tris-HCl (pH 7.4), 4% sodium dodecyl sulfate (SDS), and 10% glycerol. The protein lysis sample was boiled for 10 min at 100°C. The bicinchoninic acid protein assay kit was used for quantifying protein concentration. A total of 30 μg protein was electrophoresed in 10% or 12% SDS-polyacrylamide gel electrophoresis and transferred onto polyvinylidene difluoride membranes (Millipore) and then blocked with 5% bovine serum albumin for 1 h. The blots were then incubated with primary antibody overnight. The following day, blots were incubated with secondary antibody labeled with horseradish peroxidase for 1 h after washing three times with Tris-buffered saline with Tween 20. An electrochemiluminescence kit was used for scanning protein blots, which were analyzed by ImageLab 5.2.1 (Bio-Rad Laboratories, Hercules, CA). The following antibodies were used in this study: GAPDH (Cell Signaling Technology, 2118), p16 (Proteintech, 10883-1-AP), p19 (Proteintech, 10272-2-AP), p53 (Cell Signaling Technology, 2524), AC-p53 (Cell Signaling Technology, 2570), Sirt1 (Abcam, Cambridge, UK, ab110304), NLRP3 (Abcam, ab214185), and caspase 1 p20 (Santa Cruz Biotechnology, Santa Cruz, CA, sc-398715).
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8

Quantification of AMPK, p53, and SIRT1 Signaling

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Total AMPK, phosphorylation of AMPK (pAMPK), AcP53, FOXO1, and SIRT1 were assayed by Western blot analysis. Twenty micrograms (for AMPK, pAMPK, and FOXO1), 10 μg (for AcP53), and 40 μg (for SIRT1) of protein were loaded, and antibodies (AMPK, pAMPK, FOXO1, SIRT1 (Cell Signaling, Danvers, Mass. USA) and AcP53 (Abcam, Cambridge, Mass. USA)) were used in 1:1000 (AMPK, pAMPK, and SIRT1) and 1:2000 (AcP53, FOXO1) concentrations.
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9

Western Blot Analysis of Protein Targets

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Proteins were extracted into protein lysis buffer (50mM Tris, pH 7.4, 150mM NaCl, 10% glycerol, 2% NP-40, 1mM EDTA pH 8.0, 0.1% SDS, 0.5% NaDOC) supplemented with protease and phosphatase inhibitors. Antibodies used were: Dbc1 (Bethyl Laboratories, note: nonspecific signal at 135kD for freshly made working solution), p53 (CM5, Leica Microsystems), Puma (Sigma-Aldrich), SirT1 (Millipore), p21 and tubulin (Santa Cruz). Scd1, Fas, cleaved Caspase 3, Ac-p53, p-Akt (S473), p-Akt (T308), Akt and actin antibodies were purchased from Cell Signaling. HRP-conjugated secondary antibodies (GE Healthcare) were used for detecting ECL western blot signals.
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10

Antibody Validation for SIRT1 and Related Proteins

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Antibodies against SIRT1 (5322, Sigma‒Aldrich, St. Louis, MO, USA; sc-15404, Santa Cruz, Dallas, TX, USA; or 07-131, Millipore, Temecula, CA, USA), ISG15 (15981-1-AP, Proteintech, Rosemont, IL, USA; or HPA004627, Atlas Antibodies, Bromma, Sweden), Ac-p53 (2525, Cell Signaling, Danvers, MA, USA), phospho-p53 (9284, Cell Signaling), p53 (sc-126, Santa Cruz), DBC1 (A300-434A, Bethyl Laboratories, Montgomery, TX, USA), cleaved PARP (9541, Cell Signaling), Xpress (R910-25, Thermo Fisher Scientific), Flag M2 (F1804, Sigma‒Aldrich), V5 (R960-25, Thermo Fisher Scientific), c-Myc (C3946, Sigma‒Aldrich; or sc-40, Santa Cruz), β-actin (sc-47778, Santa Cruz), and GAPDH (MA5-15738, Invitrogen, Waltham, MA, USA) were used. Anti-V5 agarose affinity gel was purchased from Sigma‒Aldrich (A7345). Doxorubicin (D1515), camptothecin (S1288), cisplatin (S1166), and recombinant human IFN-alpha A (alpha 2a) (11100-1) were purchased from Sigma‒Aldrich, Selleckchem (Houston, TX, USA), Selleckchem, and R&D Systems (Minneapolis, MN, USA), respectively.
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