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14 protocols using mapkapk2

1

Western Blot Analysis of Signaling Proteins

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Cell lysates were prepared using a lysis buffer (50 mM Tris-Cl pH 7.4, 150 mM NaCl, 1 mM EDTA, and 1% Triton X-100) supplemented with protease inhibitors (Sigma-Aldrich). Subsequently, the proteins (50 μg) were separated by SDS-PAGE, transferred onto PVDF membranes (Bio-Rad; Hercules, CA, USA), and incubated with primary antibodies and horseradish peroxidase-conjugated secondary antibodies (Bio-Rad). Protein bands were visualized using the Miracle-Star Western Blot Detection System (iNtRON Biotechnology, Seongnam, Korea). Antibodies against NRP2 (1:1,000 dilution, #sc-13117; Santa Cruz Biotechnology, Dallas, TX, USA), phospho-FAK (1:1,000 dilution, #sc-81493; Santa Cruz Biotechnology), FAK (1:1,000 dilution, #sc-557; Santa Cruz Biotechnology), phospho-MAPKAPK2 (1:1,000 dilution, #3041; Cell Signaling Technology, Danvers, MA, USA), MAPKAPK2 (1:1,000 dilution, #3042; Cell Signaling Technology), and β-actin (1:5,000 dilution, #BS6007M; Bioworld Technology, St. Louis Park, MN, USA) were used.
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2

Integrin-Mediated Signaling Pathways

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Reagents. DMSO (Sigma, D8401), SB203580 (Calbiocam, 559389), SU6656 (Sigma, S9692), and RGD peptides (Sigma, A8052).
Antibodies. Fibronectin (BD Biosciences, 610077), α-tubulin(Sigma, T5168), β-actin (Sigma, A5441), integrin β-1 (Cell Signaling Technology, 4706), integrin β-3(D7X3P) (Cell Signaling Technology, 13166), integrin β-4 (Santa Cruz Biotechnology, sc-514426), integrin β-5 (Santa Cruz Biotechnology, sc-5402), integrin α-5 (Cell Signaling Technology, 4705), integrin α-v (Cell Signaling Technology, 4711) ERK1 (Santa Cruz Biotechnology, sc-94), p-ERK(T202/Y204) (Cell Signaling Technology, 9101), AKT (Cell Signaling Technology, 9272), p-AKT(S473) (Cell Signaling Technology, 9271), SAPK/JNK (Cell Signaling Technology, 9258), p-SAPK/JNK(T183/Y185) (Cell Signaling Technology, 9251), Smad2/3 (Cell Signaling Technology, 3102), Src (Cell Signaling Technology, 2110), p-Src(Y416) (Cell Signaling Technology, 2101), p38MAPK (Cell Signaling Technology, 9211), p-p38MAPK (Cell Signaling Technology, 9212), MAPKAPK2 (Cell Signaling Technology, 3042), p-MAPKAPK2(Thr334) (Cell Signaling Technology, 3007), and), p-paxillin (Y118) (Cell Signaling Technology, 2541).
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3

Western Blot Analysis of Protein Expression

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Protein concentrations were measured using the Pierce BCA protein assay kit. An equal amount of protein lysates was loaded onto 4–20% SDS-PAGE gels. Following electrophoresis, proteins were transferred to PVDF membranes. For detection of proteins, the membranes were incubated with the following antibodies overnight at 4 °C: SOD2 (A-2, Santa Cruz: sc-133134, 1:500 dilution); β-tubulin (9F3, Cell Signaling Technology: 2128, 1:1,000 dilution), ATP5A (Abcam: ab14748, 1:1000 dilution), β-actin (Thermo: AM4302, 1:10,000 dilution), HuR/ELAVL1 (3A2, Santa Cruz: sc-5261, 1:500 dilution), Phospho-p38 MAPK (Thr180/Tyr182, Cell Signaling Technology: 9211, 1:1000 dilution), p38 MAPK (A-12, Santa Cruz Biotechnology: sc-7972, 1:1000 dilution), MAPKAPK-2 (Cell signaling technology: 3042, 1:1000 dilution), Cox2/PTGS2 (D5H5, Cell Signaling: 12282, 1:1000 dilution). The blots were developed using SuperSignal West Femto Maximum Sensitivity Substrate (Thermo: 34096) after incubation with horseradish peroxidase (HRP)-conjugated secondary antibodies (Amersham Biosciences) for 1 h at RT.
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4

Mitochondrial Dynamics Regulation in Toxicity

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Isoniazid and SB203580 (SB) were obtained from Sigma-Aldrich (St. Louis, MO, United States). Mdivi-1, an inhibitor of DRP1, was purchased from Selleck Chemicals (Houston, TX, United States). Tetramethyl rhodamine methyl ester (TMRM), MitoTracker Deep Red FM, Hoechst 33342 and Lipofectamine RNAiMAX were obtained from Invitrogen (Grand Island, NY, United States). p38 MAPK-siRNA, a silencer negative control siRNA, and antibodies against p38 MAPK, phospho-p38 MAPK, NRF1, COX IV, cytochrome c, caspase 9, caspase 3, MFN2, DRP1, acetylated lysine, p-MAPKAPK-2, MAPKAPK-2 and β-actin were purchased from Cell Signaling Technology (Danvers, MA, United States). Antibodies against SIRT1 and Bax were obtained from Abcam (Abcam, Cambridge, United Kingdom). PGC1α antibody and protein A/G-agarose beads were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, United States). All other chemicals were of analytical grade.
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5

Antibody Sources for Cell Cycle Regulation

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Antibodies were purchased from the following sources: Cdt1 (Cat# 8064, at least two different lots were used in this study), Chk1 (Cat# 2345), phospho-Chk1 S345 (Cat# 2341), Cyclin E1 (Cat#4129), MAPKAPK-2 (Cat#), Phospho-MAPKAPK-2 T334 (Cat#3007), phospho-Histone H2A.X Ser139 (Cat#9718) from Cell Signaling Technologies; hemagglutinin (HA) (Cat#11867423001) from Roche; Geminin (Cat#sc-13015), Cdc6 (Cat#sc-9964), MCM6 (Cat#sc-9843), Cyclin A (Cat#sc-596), Cyclin B1 (Cat#sc-245) and CDK2 (Cat#sc-163) from Santa Cruz Biotechnology; MCM4 (Cat#3728) from Abcam. MCM2 antibody (Cat#A300-191A) used for co-immunoprecipitation experiment was purchased from Bethyl Laboratories. MCM2 antibody (BD Biosciences, Cat#610700) was used for analytical flow cytometry. Serum to detect CDK1 was a gift from Y. Xiong (University of North Carolina), and MPM2 antibody was a gift from R. Duronio [82 (link)] (University of North Carolina). The phosphospecific Cdt1 antibody was described in Chandrasekaran et al [17 (link)].; the third and fourth test bleeds are active for Cdt1 immunoprecipitation. Alexa 647-azide and Alexa-488-azide used in flow cytometry analyses was purchased from Life Technologies, and secondary antibodies for immunoblotting and immunofluorescence were purchased from Jackson ImmunoResearch.
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6

Western Blot Analysis of Protein Signaling

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Western blotting analysis was conducted as previously described (25 (link)). Cells were lysed with RIPA lysis buffer, and total protein concentrations were quantified using Protein Assay Kit (Bio-Rad, Hercules, CA, USA). Equal amounts of protein were separated on Mini-PROTEAN TGX gels (Bio-Rad) and transferred onto PVDF (polyvinylidene fluoride) membranes (Millipore, Billerica, MA, USA). After blocking with 5% BSA at room temperature for 30 min, the membranes were incubated with the relevant primary antibody followed by an appropriate secondary antibody. The primary antibody of p38, p-p38, MAPKAPK2, p-MAPKAPK2, HSP27 and p-HSP27 were obtained from Cell Signaling Technology (1:2000, Danvers, MA, USA). CNR1 and CNR2 antibody were purchased from Abcam (1:800, Cambridge, MA, USA). Anti-GAPDH (1:10000, Cell Signaling Technology) was used as the loading control. Western blots were developed using ECL reagent (Pierce ECL Western Blotting Substrate, Thermo Scientific).
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7

Characterization of JAK2 V617F Signaling

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OSU-A9 was provided by one of the co-authors, Dr. J.-R. Weng [9 (link)]. Identity and purity (≥99%) was verified by proton nuclear magnetic resonance, high-resolution mass spectrometry and elemental analysis. Primary antibodies for Akt, p-Akt (Ser473), ERK, p-ERK (Thr202/Tyr204), PARP, JNK, p-JNK (Thr183/Tyr185), p38 MAPK, p-p38 MAPK (Thr180/Tyr182), Caspase-3, MAPKAPK-2, p-MAPKAPK-2 (Thr334), JAK, p-JAK (Tyr1007/Tyr1008), STAT3, p-STAT3 (Ser727) were from Cell Signaling Technologies (Beverly, MA) whereas β-actin was from Sigma-Aldrich (St. Louis, MO). The p38 mitogen-activated protein kinase inhibitor SB203580 was purchased from Sigma-Aldrich. pCMV-Flag and STAT3-CA-Flag were purchased from Addgene (Cambridge, MA). The JAK2V617F-MSCV-IRES-GFP vector was kindly provided by Dr. Yen, Jeffrey J.Y. (Academia Sinica, Taiwan).
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8

Preparation and Analysis of Nuclear and Cytoplasmic Fractions

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To separate the cell cytoplasmic and nuclear fractions, cells were first lyzed with low salt buffer (20 mM Hepes pH 7.9, 10% Glycerol, 1.5 mM MgCl2, 0.05 % NP40, protease inhibitors) on ice for 5 minutes and then centrifuged at 4000rpm for 5 minutes at 4°C. Supernatant was collected as cytoplasmic fractions, the pellet was then lyzed with high salt buffer (20 mM Hepes pH 7.9, 10% Glycerol, 1.5 mM MgCl2, 500mM NaCl, 0.05 % NP40, protease inhibitors) to collect the nuclear fractions. Co-immunoprecipitation and Western blot were performed as previously described (Wang et al., 2014a (link)). The following antibodies were used for Western blotting: METTL3 (Proteintech,15073-1-AP); β-Tubulin (Abcam, ab6046); EGFR (Cell Signaling Technology, #2232); TAZ (BD Pharmingen, 560235); MAPKAPK2 (Cell Signaling Technology, #3042); DNMT3A (Abcam, ab13888); β-Actin (Abcam, ab119716); Fibrillarin (Abcam, ab4566); CBP80 (Choe et al., 2012 (link)); CTIF (Choe et al., 2012 (link)); eIF4E (Cell signaling technology, #2067); eIF3b (Santa Cruz Biotechnology,sc-16377); eIF4AI (Abcam, ab31217); eIF4GI (Cell signaling technology, #2498); FLAG (Sigma, A8592); METTL14 (Sigma, HPA038002); WTAP (Proteintech Group 60188-1-Ig); YTHDF1 (Abcam, ab99080); YTHDF2 (Proteintech, 24744-1-AP).
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9

Western Blot Analysis of Signaling Proteins

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Cells lysates were separated on 15% polyacrylamide gels and transferred onto nitrocellulose for 2 h at 250 mA, followed by blocking with 5% (w/v) nonfat dried milk for 1 h. Blots were incubated with the appropriate primary antibody with dilution according to the manufacturers’ instructions (beta-actin, Mab AC-40, Sigma-Aldrich, St. Louis, MO, USA; dilution 1:5000); MAPKAPK-2 (Cell signaling 3042, dilution 1:1000); pT222-MAPKAPK-2 (Cell signaling 3316, dilution 1:1000); PAK2 (Cell signaling 2608, dilution 1:1000); phospho-S144/141-PAK1/2 (Abcam ab40795; dilution 1:2000); Rac1 (BD Transduction Laboratories 610650, clone 102; dilution 1:1000); Rac1(Millipore 05-389, clone 23A8; dilution 1:1000) in buffer B (50 mM Tris-HCl, pH 7.2, 150 mM NaCl, 5 mM KCl, 0.05% (w/v) Tween 20) for 18 h and subsequently for 2 h with a horseradish peroxidase-conjugated secondary antibody (mouse: Rockland 610-1034-121; dilution 1:3000; rabbit Rockland 611-1302; dilution 1:3000). For the chemiluminescence reaction, ECL Femto (Fisher Scientific, Schwerte, Germany) was used. The signals were analyzed densitometrically using the KODAK 1D software (2004, Rochester, MN, USA).
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10

Comprehensive Protein Expression Analysis

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ELISA for IFN-γ and IL-12p70 production was performed by ELISA kits (R&D Systems). For Westernblot, anti-mouse p38α (Cat#9218), p38γ (Cat#2307), p38 (Cat#8690), p-p38 (Cat#4631), MAPKAPK-2 (Cat#3042), pMAPKAPK-2 (Cat#3041), RelA (Cat#4764), RelB (Cat#4954), p52 (Cat#4882), GAPDH (Cat#2118), PARP (Cat#9532), C/EBP-β (Cat#3087), pC/EBP-β (Cat#3084), PPARγ (Cat#2430), pStat3 (Cat#9145), Stat3 (Cat#12640), pSmad3 (Cat#9520), Smad3 (Cat#9523), IκB-α (Cat#4812) and β-actin (Cat#4970) from Cell Signaling (1:1000 dilution), and anti-mouse p38β, (Cat#sc-6187), p38δ,(Cat#sc-7587), p50 (Cat#sc-7178) and c-Rel (Cat#sc-70) from Santa Cruz Biotechnology (1:250 dilution) were used.
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