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32 protocols using p16ink4a

1

Western Blot Protein Expression Analysis

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Briefly, protein was mixed 1:1 with 2×SDS loading buffer and incubated at 100°C for 4 min. Then, the protein was electrophoresed in 10–12% SDS-polyacrylamide gel and transferred electrophoretically onto a polyvinylidene difluoride microporous membrane (Millipore, Billerica, MA, USA). Membranes were incubated with primary antibody overnight [p16(INK4a): 1:200, Santa Cruz Biotechnology, USA; Sca-1: 1:200, Biolegend, USA; eNOS: 1:1000, Proteintech, USA), and then washed carefully with Tris-buffered-saline with Tween-20 (TBST) followed by re-incubation with secondary antibodies (1:3000; 1 h). After washing with TBS-T again, immunoreactive bands were detected using ECL chemiluminescent substrate (Thermo, USA).
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2

Quantitative Protein Analysis of ATM-KAP1 Pathway

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MEFs were treated with either KU-55933 (10 μM, Selleckchem) or vehicle for 72 hours prior to harvesting for analysis of protein expression. Cell lysates were prepared with RIPA buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM Na2EDTA, 1 μM EGTA, 1% NP-40, 1% sodium deoxycholate, 2.5 μM sodium pyrophosphate, 1 μM β-glycerophosphate, 1 μM Na3VO4 and 1 μg/ml leupeptin), supplemented with 1X of protease inhibitor cocktails (Sigma) and Halt phosphatase inhibitor cocktail (Thermo #78420). Snap-frozen liver and kidney samples were homogenized using FastPrep-24 instrument in RIPA buffer. Equal amounts of proteins (40 μg) were resolved on 4-15% Mini-PROTEAN TGX precast protein gels (Bio-Rad). Primary antibodies used are as follows: p-ATM Ser 1981 (cell lysates: Rockland cat. no. 200-301-400; tissue lysates: Santa Cruz sc-47739), ATM (CST #2873), p-KAP1 Ser 824(Abcam ab70369), KAP1 (Abcam ab22553), γ-H2AX (Novus NB100-384), PARP1 (CST #9532), p-p65 Ser 536 (CST #3033), p65 (CST #8242), p-IκBα Ser 32/36 (CST #9246), IκBα (Santa Cruz sc-371), p16INK4a (Santa Cruz sc-1207), p21Cip1 (Santa Cruz sc-6246), LaminA/C (Santa Cruz sc-20681), anti-tubulin (CST #2146), and GAPDH (CST #5174). Blots were exposed to X-ray film in a dark room or developed on iBright™ FL1000 Imaging System (Figure 1E and 1F). Protein levels were quantified by Image J software.
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3

Anticancer Effects of 20(S)-Ginsenoside Rg3

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20(S)-ginsenoside Rg3 was obtained from the National Institute for the Control of Pharmaceutical and Biological Products (Beijing, People’s Republic of China), and the purity was at least 95% as determined by HPLC (high performance liquid chromatography). 20(S)-Rg3 was dissolved in dimethyl sulfoxide (DMSO) in a 400 mM stock solution and stored at −20°C, and diluted with fresh complete medium immediately before use. An equal volume of DMSO (final concentration <0.1%) was added to the controls.
3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide (MTT), Hoechst 33342, Rhodamine 123, and Cycloheximide (CHX) were purchased from Sigma-Aldrich (St Louis, MO, USA). Annexin V/PI apoptosis kit was purchased from Invitrogen (Carlsbad, CA, USA). Primary antibodies against Bad, Bax, Bcl-2, Bcl-XL, cleaved-caspase 3 (Asp175), murine double minute 2 (MDM2), and β-actin were purchased from Cell Signaling Technology (Beverly, MA, USA). p53, p16INK4A, and pRB antibodies were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA). p21CIP1 antibody was obtained from BD Biosciences (San Diego, CA, USA). Cyclin A and Cyclin B1 antibodies were purchased from Epitomics (Burlingame, CA, USA). PCNA (proliferating cell nuclear antigen) antibody was obtained from Abcam (Cambridge, UK).
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4

Immunoblotting Analysis of Stem Cell Markers

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Immunoblots were performed following standard procedures. Equal amounts of protein (20 μg) were separated on 15% SDS polyacrylamide gels and blotted onto nitrocellulose membranes (BioRad). Primary antibodies were SOX9 (Millipore), SOX2 (Millipore), P-p38MAPK (Cell Signalling), total p38MAPK (Santa Cruz), p16Ink4a (Santa Cruz) and β-actin (Sigma). Secondary antibodies were HRP-linked anti-mouse or rabbit (DAKO). Detection was performed by chemiluminescence using ECL (Amersham).
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5

Endothelial Cell Protein Extraction and Western Blot

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Briefly, EPCs were washed 3 times with ice-cold phosphate-buffered saline (PBS), then lysed in RIPA lysate (Applygen Technologies Inc, Beijing, China) for 30 min on ice. The solution of EPCs was centrifuged at 4°C and 12000×g for 5 min. BCA protein quantitation kit (Wellbio Inc, Changsha, China) was used for protein measurement. Protein was mixed 1: 1 with 2×SDS loading buffer (20% glycerol, 4% sodium dodecyl sulfate, 3.12% dithiothreitol, 0.2% bromphenol blue, and 0.1 mol/l Tris HCl, pH 6.8, all from Sigma, Santa Clara, CA, USA), and incubated at 100°C for 4 min. Equal amounts of protein for each sample were separated by 10–12% SDS-polyacrylamide gel run at 120V for 90 min and blotted onto a polyvinylidene difluoride microporous membrane (Millipore, Billerica, MA, USA). Membranes were incubated overnight with primary antibody (eNOS: 1: 1000, Proteintech, Chicago, IL, USA; p16(INK4a): 1: 200, Santa Cruz Biotechnology, Santa Cruz, TX, USA), and subsequently washed 3 times with Tris-buffered-saline with Tween (TBS-T) and visualized following incubation with horseradish peroxidase-conjugated secondary antibody (1: 3000) for 1 h, followed by washing with TBS-T again. Immunoreactive bands were developed using an enhanced chemiluminescent substrate (Thermo, Waltham, MA, USA). After exposure, the films were scanned and analyzed using Quantity One (Bio-Rad, CA, USA).
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6

Western Blot Analysis of Cell Signaling

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Cells were washed in PBS and then lysed in NP40 lysis buffer (50 mM Tris pH 7.5, 150 mM NaCl, 0.5% NP40, and protease and phosphatase inhibitors). 50–80 µg of protein were separated by SDS-polyacrylamide electrophoresis (SDS-PAGE) and transferred onto nitrocellulose membranes (Amersham Hybond ECL) using a semidry blotting system. The blots were incubated with antibodies specific to α-tubulin (Cell Signaling 2125, (11H10) 1:3,000), p16Ink4A (Santa Cruz Biotechnology sc-1207, 1:500), p-Hsp27 (Ser82) (Cell Signaling 2401, 1:1,000), p-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (Cell Signaling 4370 (D13.14.4E), 1:1,000), p-Mek1 (Ser222) (Santa Cruz Biotechnology sc-293106, 1:200), p-p38 (Thr180/Tyr182) (Cell Signaling 4511 (D3F9), 1:1,000), cyclin A (Santa Cruz Biotechnology sc-596, 1:200), p38α (Cell Signaling 9218, 1:1,000), p-Tgfbr1 (Ser165) (Abcam ab112095, 1:500) and p-Atf2 (Thr71) (Cell Signaling 9221, 1:1,000), followed by peroxidase-conjugated secondary antibodies. Images were detected by ChemiDoc MP Imaging System (Bio-Rad).
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7

Protein Expression Analysis Protocol

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Total protein extracts and western blot analysis were performed as described before [18 (link)]. The primary and secondary antibodies used were: p16INK4a 1:500 (Santa Cruz; sc-1207), p21Cip1 1:1000 (Abcam; ab109520), p-H2AX (Ser139) 1:1000 (Millipore; 05-636), p-p53 (Ser15) 1:1000 (Abcam; ab1431), Hif1a 1:1000 (BD Transduction Laboratories; 610958), α-tubulin 1:5000 (Sigma-Aldrich; T9026), Sox2 1:1000 (Abcam; ab97959), Nanog 1:500 (Santa Cruz; sc293121), cMyc-tag 1:1000 (Origene; TA150014), Oct3/4 1:500 (Santa Cruz; sc-5279), Tfcp2l1 1:1000 (Novus Biologicals; AF5726), goat anti-rabbit IgG (horseradish peroxidase, HRP) 1:5000 (Abcam; ab97051), rabbit anti-mouse IgG (HRP) 1:5000 (Abcam; ab97046) and rabbit anti-goat IgG (HRP) 1:5000 (Abcam; ab97100). See uncropped WB in supplementary material.
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8

Western Blot Analysis of Cellular Proteins

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Cells were washed with PBS and lysed in NP-40 lysis buffer (150 mM NaCl, 1.0% NP-40, 50 mM Tris–HCl [pH 8.0], 1 mM phenyl- methylsulfonyl fluoride, 1 mg/ml leupeptin, 1 mM sodium orthovanadate, 1 mM EDTA). Lysates were cleared by centrifugation, 10,000 rpm for 10 minutes. Samples corresponding to 50–80 µg of protein were separated on 6%, 8%, 10% or 15% SDS–PAGE gels and transferred to Immobilon-P membranes (Millipore). Western blot analysis was accomplished according to standard procedures using ECL reagent (GE Healthcare Piscataway, NJ).
The following primary antibodies were used: HIF-1α (1∶250, BD Biosciences Pharmingen, San Diego, CA), p53, p21CIP1, p16INK4a, Mif (1∶250, Santa Cruz Biotechnology, San Diego, CA, USA) and β-actin (1∶5000, T4026, Sigma). DNA damage response was analyzed using DNA Damage Antibody Sampler Kit (1∶1000, Cell Signaling Technology, Beverly, MA) including phospho-ATR (Ser428) phospho-ATM (Ser1981)(D6H9), phospho-Chk1 (Ser296) phospho-Histone H2A.X (Ser139) (20E3) phospho-Chk2 (Thr68) and. Phosphorylation of Rb protein was analyzed by Rb Ab (Ser807/811) (1∶1000, Cell Signaling Technology, Beverly, MA). HRP-conjugated secondary antibodies were purchased from GE Healthcare (Piscataway, NJ).
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9

Western Blot Analysis of Cell Signaling

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Cells were treated with adriamycin (Sigma-Aldrich) or etoposide (Sigma-Aldrich), and SDS protein samples were then prepared by directly lysing the cells in SDS sample buffer (Elpisbiotech. Inc., Daejeon, Korea) after washing with ice-cold phosphate-buffered saline (PBS).
Western blots were conducted using antibodies against MDM2 (Santa Cruz Biotechnology, Inc., #sc-965), p21WAF1 (Santa Cruz Biotechnology, Inc., #sc-6246), p53 (Santa Cruz Biotechnology, Inc., #sc-126), p16INK4A (Santa Cruz Biotechnology, Inc., #sc-1661), p14ARF (Cell Signaling #74560), and GAPDH (Cell Signaling #2118).
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10

Ginsenoside Rg1 Modulates Cellular Senescence

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Ginsenoside Rg1 (Purity = 98.3%, RSZD-121106) was obtained from Xi’an Haoxuan Biological Technology Co., Ltd. (Xi’an, China). d-galactose was purchased from Shanghai Puzhen biological science and Technology Co., Ltd. (Shanghai, China). Fetal bovine serum (FBS) and Iscove’s Modified Dulbecco’s Medium (IMDM) were purchased from Gibco (Waltham, MA, USA). The Anti-Sca-1+ Micro Bead Kit was purchased from Miltenyi Biotech Co. (Bergisch Gladbach, Germany). The SA-β-gal Staining and Reactive Oxygen Species Assay Kits were purchased from the Beyotime Institute of Biotechnology (Shanghai, China). The SOD, GSH-px, T-AOC and MDA kits were obtained from Nanjing Jiancheng Bioengineering Institute (Nanjing, China). The methylcellulose semi solid culture medium for CFU-mix was purchased from Stem Cell Technologies (Vancouver, BC, Canada). The antibodies against β-catenin, GSK-3β, Phospho-GSK-3β, TCF-4, and r-H2A.X were obtained from Cell Signaling Technology (Danvers, MA, USA). The antibodies against p16INK4a, Rb, p53, p21Cip1/Waf1, β-actin and Histone 2A were purchased from Santa Cruz (San Cruz, CA, USA), and Anti-4-HNE antibody was purchased from Abcam (Cambridge, MA, USA). The Mouse ELISA Kit for 8-OHdG or AGEs was obtained from Shanghai Yuanye Bio- Technology Co., Ltd. (Shanghai, China).
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