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40 protocols using total s6

1

Protein Expression Profiling by Western Blot

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Blotting was performed as per our previous reports32 (link)33 (link). Briefly, total protein of lysates was extracted and equal amount of protein was loaded onto 10% sodium dodecyl sulphate polyacrylamide gel for electrophoresis. Gels were subsequently transferred to nitrocellulose membrane. The membranes were blockaded for 1 h with 5% non-fat milk. Primary antibodies against VHL (Abcam), HIF1α (Abcam), HIF2α (Abcam), SETD2 (Abnova), H3 (Abcam), H3K36me2 (Lys36, Cell Signaling), H3K36me3 (Lys36, Cell Signaling), PI3 Kinase p110β (Cell Signaling), pS6 (Ser235/236, Cell Signaling), total S6 (Cell Signaling), pAkt (Ser473, Cell Signaling) and total Akt (Cell Signaling) were then added and membranes were kept incubating at 4°C overnight. Corresponding secondary antibodies were applied followed by electrochemiluminescence (ECL) processing.
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2

Prostate Cancer Cell Signaling Assay

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LNCaP95 cells were serum-starved for 24hr, followed by treatment with DMSO, EPI-002 (25uM), enzalutamide (10 uM), BEZ235 (15nM) or a combination for 1hr prior to addition of R1881 or EtOH for 48hr. Antibodies used were: AR (1:1000; Santa Cruz), AR-V7 (1:400; Precision), p110α (1:500; BD Bioscience), p110β (1:1000; abcam), p100γ (1:1000; abcam), p110δ (1:1000; abcam), UBE2C (Boston Biochem; 1:1000), PTEN (1:1000), pS6 (1:2000), pAktThr308 (1:1000), pAktSer473 (1:2000), p4EBP1 (1:1000), total-Akt (1:1000), total-S6 (1:1000), total-4EBP1 (1:1000), pERK/MAPK (1:1000), total-ERK/MAPK (1:1000) from Cell Signaling technology (Danvers, MA). β-actin (1:10,000, Abcam) was used as a loading control.
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3

Western Blot Protein Expression Analysis

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Cells were collected and lysed in RIPA buffer (50 mM Tris-HCl, pH 7.5; 150 mM NaCl; 0.5% NP-40; 50 mM NaF with protease inhibitors) and incubated on ice for 30 min. Lysates were centrifuged at 20,817g at 4 °C for 10 min and supernatant was collected. Protein concentration was determined using the Bradford assay (Bio-Rad Laboratories, Hercules, CA). Equal amounts of protein samples were mixed with SDS Laemmli loading buffer, boiled and electrophoresed using NuPAGE Bis-Tris Gels (Life Technologies), then transferred onto PVDF membranes (Millipore). Blocking was performed for 45 min using TBST supplemented with 5% non-fat dry milk and blotting performed with primary antibodies at 4 °C for 16 h. The following antibodies were used: ADSL (Abcam #ab154182), GMPS (Cell Signaling #14602), PRPS1 (Abcam #ab154721), MYC (N-262, Santa Cruz #sc-764), total AKT (Cell Signaling #4691), phospho-AKT (S473, Cell Signaling #9271), total S6 (Cell Signaling #2317), phospho-S6 (235/236, Cell Signaling #4858), phospho-S6 (240/242, Cell Signaling #5364), total p70 S6K (Cell Signaling #2708), phospho-p70 S6K (Cell Signaling #9234) and α-tubulin (Sigma #T6074). All antibody validation information is available in the product’s manual. For western blotting, the dilution was 1:500 for MYC antibody and 1:1,000 for all other antibodies.
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4

Nuclear Protein Extraction and Immunoblotting

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Cells were lysed in NP-40 buffer (40 mM HEPES, pH 7.4; 400 mM NaCl; 1 mM EDTA, pH 8.0; 1% NP-40 (CA-630, Sigma); 5% glycerol; 10 mM pyrophosphate; 10 mM β-glycerophosphate; 50 mM NaF; 0.5 mM orthovanadate) containing Protease Inhibitor Cocktail (Sigma) and 1 mM DTT. Nuclear isolation was performed with a Nuclear Extract Kit (40010, Active Motif, Carlsbad, CA, USA), with 10 μg/ml ALLN (208719, Millipore, Bedford, MA, USA) treatment 20 min prior to isolation, and ALLN added to the hypotonic and lysis buffers. The nuclear fraction was washed with hypotonic buffer prior to lysis.
Antibodies used for immunoblots recognized SREBP1 (sc-8984, Santa Cruz, Santa Cruz, CA, USA), SREBP2 precursor and processed C-terminus (557037, BD, Franklin Lakes, NJ, USA), SREBP2 mature N-terminus (30682, Abcam, Cambridge, MA, USA), Actin (A5316, Sigma), and from Cell Signaling Technologies (Danvers, MA, USA): ACC1 (3676), FASN (3180), SCD (2438), HA (2367), P-Akt-T308 (9275), P-Akt-S473 (4051), Total-Akt (4691), P-S6K1-T389 (9234), Total-S6K1 (2708), P-S6-S240/S244 (2215), Total-S6 (2217), 4E-BP1 (9644), Ras (3965), P-Erk1/2-T202/Y204 (9106), Total-Erk1/2 (9102), Lamin A/C (2032), Histone H3 (4499).
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5

Antibody Staining and Quantification

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Antibodies purchased from Cell Signaling Technology were used at a dilution of 1:1000 and include phospho‐S6 ribosomal protein (S235/236) (D57.2.2E) XP (R) (rabbit monoclonal, #4858), phospho‐AKT (Ser 473) (D9E) XP(R) (rabbit mAb, #4060), phospho‐p44/42 MAPK (T202/Y204) (rabbit, #9101), total AKT (rabbit, #9272), total MAPK (mouse, #9107), total S6 (rabbit, #2217), Mcl‐1 (rabbit, #5453), Bcl‐xL (rabbit, #2764), Bcl‐2 (human specific, #2872) and beta‐tubulin (rabbit polyclonal, #2146). Anti‐GAPDH (14C10) (rabbit mAb, #2118) (Cell Signaling Technology) was used at a dilution of 1:3000.
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6

Western Blot Analysis of Cellular Proteins

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E-Cadherin antibody was obtained from BD Biosciences. Vimentin antibody was obtained from Sigma. Antibodies to cyclophilin, GSTP1, β-actin, phospho-AMPK α (Thr172), AMPK α, phospho-ACC (Ser79), ACC, phospho-S6, total S6, phospho-JNK (Thr183/Tyr185), JNK, and GAPDH were obtained from Cell Signaling Technology. FLAG antibody was obtained from Cayman Chemicals.
Cells were lysed in lysis buffer (CST) containing both protease and phosphatase inhibitors. Proteins were resolved by electrophoresis on 4–15% Tris-glycine precast Mini-PROTEAN TGX gel (BioRad Laboratories) and transferred to nitrocellulose membranes using the iBlot system (Invitrogen). Blots were blocked with 5% nonfat milk in Tris-buffered saline containing Tween-20 (TBST) solution for 1 hour at room temperature, washed in TBST, and probed with primary antibody diluted in recommended diluent per manufacturer overnight at 4°C. Following washes wit h TBST, the blots were incubated in the dark with a IR-linked secondary antibody at room temperature for 1 hour. Blots were visualized using an Odyssey Li-Cor scanner after additional washes.
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7

Antibody Identification in Protein Analysis

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The rabbit anti-APAP-AD antibody was a kind gift from Dr. Lance Pohl (National Heart, Lung and Blood Institute, USA).13 (link) The other antibodies were: CYP2E1 (#ab28146) from Abcam (Cambridge, UK), p62 (#H00008878-M01) from Abnova (Taipei, China), phospho-S6 (#4858), total S6 (#2217), phospho-JNK (#4668), and GAPDH (#2118) from Cell Signaling Technology (Danvers, MA, USA); β-actin (#a5441) from Sigma-Aldrich (St. Louis, MO, USA), total JNK (#554285) from BD Pharmingen (Franklin Lakes, NJ, USA); proliferating cell nuclear antigen (PCNA) (#SC-56) from Santa Cruz Biotechnology (Dallas, TX, USA). The rabbit anti-microtubule-associated protein 1 light chain 3 (LC3) antibody was described previously.22 (link) The secondary antibodies were HRP-conjugated goat-anti-rabbit (#111-035-045), and HRP-conjugated goat-anti-mouse (#115-035-062) were from Jackson ImmunoResearch (West Glove, PA, USA). All other reagents were either from Sigma (USA) or Thermo Fisher Scientific (USA).
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8

Quantitative Western Blot Analysis of Oncogenic Signaling

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Freshly harvested cancer cells or xenograft tumors were lysed with 1X cell lysis buffer (Cell Signaling Technologies, Danvers, MA) containing protease and phosphatase inhibitors (Roche, Indianapolis, IN). Subsequently, 30–40 μg of protein was run on 4–12% Bis-Tris gels (Thermo Fisher, Waltham, MA), and protein was transferred onto nitrocellulose membranes (Thermo Fisher). Membranes were blocked for one hour using Licor Odyssey Blocking Buffer (Lincoln, NE) before immunoblotting using the following antibodies (all from Cell Signaling Technology, Danvers, MA, USA): pEGFR (#3777), total EGFR (#2239), pMet (#3077), total Met (#3127), pAKT (#4060), total AKT (#9272), pERK (#9101), total ERK (#4695), pS6 (#2211), and total S6 (#2317). Western blots were processed using Licor Odyssey Imaging System, and densitometry was performed using Licor Odyssey Imaging System software.
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9

Phospho-ACC and AMPK Pathway Analysis

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The compounds used in this study were dissolved directly in DMEM and the pH corrected to pH7.4. The phospho-acetyl-CoA carboxylase (ACC) Ser 79 antibody was from the Division of Signal Transduction Therapy at the University of Dundee. The total ACC, total AMPKα, phospho-AMPKα Thr 172, total S6, phospho-S6 Ser 240/244, phospho-p70S6K Thr 389, total IκB, pNF-κB, total IKKα, and total IKKβ antibodies for immunoblotting were from Cell Signaling Technology. Actin antibody was from Merck. Antibodies used in the AMPK activity assays were a generous gift from Prof D. Grahame Hardie at the University of Dundee. Chemical structures were drawn using ChemSketch. BI605906 was a generous gift from Prof Sir Philip Cohen (MRC Protein Phosphorylation and Ubiquitylation Unit, Dundee).
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10

Investigating Autophagy and MAPK Signaling

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KL and KP TDCLs were treated with nutrient rich RPMI media containing vehicle, HCQ, trametinib or their combination for 8 h. Media were aspirated and the cells were rinsed with PBS twice. Cell lysates were collected using the Tris lysis buffer. Protein concentration was assessed using the Bio-Rad BCA reagent. The following antibodies were used for Western blots: LC3 (Novus Biologicals, NB600-1384), total ERK (Cell Signaling, 4695), phosphorylated ERK (Cell Signaling, 9101), total S6 (Cell Signaling, 2217), phosphorylated S6 (Cell Signaling, 4858), and β-actin (Sigma, A1978). LC3 quantification was performed using Image Lab software.
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