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14 protocols using p raf

1

Comprehensive Protein Analysis via Western Blot

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Western blot was conducted as previously described [23 (link)]. Primary antibodies against Cyclin-D, p-Rb, Rb, Capase 3, p-STAT3, STAT3, LMNB1, p-JAK, JAK, p-Raf, Raf, p-MEK, MEK, p-ERK, ERK, p-AKT, and AKT were purchased from Cell Signaling Technology. Antibodies against MVP and GAPDH were purchased from Santa Cruz Biotechnology. Quantification was performed with Image J.
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2

Western Blot Analysis of Signaling Proteins

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Western blot analysis was performed as previously described[4] (link). Primary antibodies against p44/42 MAPK (Erk1/2) (Thr202/Tyr204), pAkt (Ser-473), total ERK, AKT, pRaf, and GAPDH purchased from Cell Signaling Technology (Beverly, MA, USA). The SP1 antibody was purchased from Upstate Biotechnology (Lake Placid, NY, USA). The K-Ras, c-Myc, pRb, and E2F6 antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). The anti-LRRC4 monoclonal antibody was generated in our lab. The intensity of protein fragments was quantified using Chemical-QDocTM XRSt (Bio-Rad).
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3

Comprehensive Molecular Signaling Profiling

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A549 and H1299 cells were purchased from the American Type Culture Collection (ATCC, Philadelphia, PA, USA). Antibodies used for WB are listed as following: β-actin (Abgent, San Diego, USA), N-Cadherin, p-FAK, FAK, MMP-9, Cleaved PARP, Cleaved caspase-9, Cleaved caspase-8, Cleaved caspase-7, Cleaved caspase-3, Bcl-2, Bcl-xl, Bad, Bax, Cyto-c, γ-H2AX, p53, p21, Cdc25A, p-Raf, Raf, p-MEK, MEK, p-ERK, ERK, p-PI3P, PI3P, p-AKT, AKT (Cell Signaling Technology, Beverly, MA, USA), p-ATM, p-CHK2, CDK2 (Abcam Inc., Cambridge, MA). Celecoxib(≥98%,HPLC), metformin(purity: > 99.9%), and pifithrin-α were purchased from Sigma (St. Louis, USA).
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4

Protein Extraction and Western Blot Analysis in Gastric Cancer

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Protein was extracted from gastric cancer cell lines using RIPA lysis buffer containing proteinase inhibitor. The protein concentration of the lysates was measured with the Protein BCA Assay Kit (Bio-Rad, USA). For the Western blot assay, 20 µg of protein mixed with 2×SDS loading buffer was loaded per lane, separated by 12% SDS-polyacrylamide gel electrophoresis and transferred to polyvinylidene difluoride membranes (Millipore, USA). To block nonspecific binding, membranes were incubated at room temperature for 1 h with 5% skim milk powder, followed by a 12-h incubation at 4°C with antiserum containing antibodies against c-Src (B-12) (Santa Cruz Biotechnology sc-8056, Santa Cruz, CA, USA), p44/42 MAPK (Erk1/2; Thr202/Tyr204), total ERK, AKT, pRaf, and β-actin (Cell Signaling Technology, Beverly, MA, USA). Ras activity was detected using the Ras Activation Assay Kit from Upstate-Millipore (17–218). A peroxidase-conjugated secondary antibody (1∶5000 dilution) and ECL Western blotting detection reagents (New England Biolabs, USA) were used to visualize the target proteins, which were quantified with a Bio Image Intelligent Quantifier 1-D (Version 2.2.1, Nihon-BioImage Ltd., Japan). An anti-β-actin antibody (Boster, Wuhan, China) was used as a protein loading control.
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5

Antibody Profiling of Signaling Pathways

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The following antibodies were used in this study: β‐actin (Santa Cruz Biotechnology, Dallas, TX, USA), GST‐π, P‐gp, MDR1, p‐Raf, Raf, p‐MEK, MEK p‐ERK, ERK, and CYR61 (Cell Signaling Tech, Danvers, MA, USA). U0126 was obtained from Selleck (Selleck, Shanghai, China). Temozolomide was obtained from Sigma‐Aldrich (St. Louis, MO, USA).
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6

Evaluating Drug-Induced Signaling Pathways

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HSC-T6 cells were seeded in six-well plates at a density of 2 × 105 cell/well and incubated with 68 μM (IC50) and 34 μM (half IC50) of WM130 and 68 μM of M19 for 24 h; PBS was used as blank control. Cells were lysed in radio immunoprecipitation assay (RIPA) lysis buffer supplemented with phosphatase and protease inhibitors. Equal amounts of protein were separated by SDS-PAGE and transferred to PVDF membranes. The membranes were then blocked with 5% nonfat dry milk and incubated with the primary antibodies, including the rabbit antibodies to rat AKT, p-AKT, ERK, p-ERK, EGFR, p-EGFR, and p-Raf (Cell Signaling Technology, Danvers, MA), the mouse antibodies to rat TGF-β1, α-SMA (Abcam Inc. Cambridge, MA) and p-Smad (Santa Cruz Biotech Inc., CA), and the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) antibody (Kangchen Bio-tech, Shanghai, China), followed by incubation with the secondary antibodies, horseradish peroxidase-conjugated sheep anti-mouse immunoglobulin (Ig) G or sheep anti-rabbit IgG (Abcam Inc. Cambridge, MA). Blots were developed using an enhanced chemiluminescence detection kit (Beyotime Biotechnology, Shanghai, China). The agarose gel bands were scanned for gray density analysis relative to the loading control by ImageJ software.
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7

Western Blot Analysis of EMT-related Proteins

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Total proteins from cultured cells were lysed using RIPA buffer supplemented with protease and protease inhibitors (Roche, Mannheim, Germany). An equal amount of 50 μg proteins were fully electrophoresed on 6–10% SDS polyacrylamide gels and transferred to polyvinylidene difluoride membranes. The membranes were incubated with primary antibodies at 4 °C overnight after blocked with 5% non-fat milk at room temperature for 1 h. The primary antibodies against GAPDH were obtained from Abcam (Cambridge, MA, USA). The antibodies against E-cadherin, N-cadherin, Vimentin, Slug, Zeb1, NRG1, ERBB2, p-ERBB2, ERBB3, p-ERBB3, MEK1, p-MEK1, Erk, p-Erk, Raf, p-Raf, Fra-1, Fra-2, c-Fos, FosB, c-Jun and JunB (diluted at 1:1000 ratio) were purchased from Cell Signaling Technology (Beverly, MA, USA). Then, the membranes were incubated with goat anti-rabbit or anti-mouse secondary antibody (diluted at 1:5000 ratio) and then detected with ECL Detection System (Thermo Scientific, Rockford, IL, USA).
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8

Optimized Protein and RNA Extraction Protocol

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Oligonucleotide primers for both convention and Real-Time PCR were synthesized by Integrated DNA technologies (Coralville, Iowa) and are listed in Supplementary Table S1. Total RNA and proteins were isolated from various using standard protocols as we described [11 (link)]. Total RNA was subjected to conventional PCR and/or Real-Time PCR analyses using a master mix from Bio-Rad Laboratories (Hercules, CA). Protein extracts were subjected to immunoblot analysis using with antibodies against Alix, Hrs, NA+-K2+ ATPase, Rab5, Ras, p-Raf, Raf, p-ERK, and ERK (Cell Signaling Technology, Danvers, MA), TSG101, CD9, CD81, CD63, and GAPDH (Santa Cruz Biotechnology, Dallas, TX), Rab27a (Proteintech, Chicago, IL). Immune complexes were detected with appropriate secondary antibodies from Santa Cruz Biotechnology (Dallas, TX) and chemiluminescence reagents (Pierce, Rockford, IL, USA). Immunoblot signals were captured using the Image Quant Las 300 (GE Healthcare, Piscataway, NJ). Densitometric analysis was performed using ImageJ (NIH, Bethesda, MD, USA, http://imagej.nih.gov/ij/)
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9

Western Blot Analysis of Protein Expression

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The HRVECs were lysed with ice-cold RIPA buffer and the concentration of protein was determined using a BCA protein assay reagent kit (Beyotime, China). The proteins (15 μg) were separated by dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred onto a polyvinylidene fluoride (PVDF) membrane. Then, the membrane was blocked with 5% skimmed milk for 2 h at room temperature. The PVDF membranes were then incubated overnight at 4°C with the following primary antibodies to: proliferating cell nuclear antigen (PCNA; Cell Signaling Technology, Boston, MA, USA), Ki67 (Santa Cruz Biotechnology, CA, USA), (p-) Raf (Cell Signaling Technology, Boston, MA, USA), (p-) MEK (Cell Signaling Technology, Boston, MA, USA), (p-) ERK (Cell Signaling Technology, Boston, MA, USA), VE-cadherin (Cell Signaling Technology, Boston, MA, USA), Frizzed (Abcam Company, Cambridge, UK), β-catenin (Cell Signaling Technology, Boston, MA, USA), MMP-2 (Abcam Company, Cambridge, UK), MMP-9 (Abcam Company, Cambridge, UK) and GAPDH (Cell Signaling Technology, Boston, MA, USA). Followed by being incubated with a horseradish peroxidase (HRP)-labeled secondary antibody (Abcam, Cambridge, MA, USA). The results were visualized with an enhanced chemiluminescence (ECL) detection kit. ImageJ software (National Institutes of Health, Bethesda, MD, USA) was used to quantify the density of the bands.
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10

Protein Analysis of PDCs

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Total proteins from PDCs were isolated using RIPA buffer (Sigma-Aldrich, St. Louis, MO, USA) containing a protease inhibitor cocktail (Roche, Mannheim, Germany) and phosphatase inhibitor cocktail (Roche), and protein concentration was determined using a Quick Start Bradford Protein Assay (Bio-Rad, Hercules, CA, USA). Aliquots containing 30 μg of protein were subjected to 10% SDS-polyacrylamide gel electrophoresis and electrotransferred to nitrocellulose membranes. The membranes were blocked with 5% nonfat dry milk in Tris-buffered saline containing 0.1% v/v Tween 20 and probed overnight at 4°C with specific antibodies against the following proteins: p-EGFR, p-RAF, RAF, p-MEK, MEK, p-ERK, ERK, p-Rb1, Rb1, P-AKT, AKT (Cell Signaling Technology, Beverly, MA, USA), and beta actin (Sigma Aldrich). Horseradish peroxidase-conjugated anti-rabbit or anti-mouse IgG (Vector, Burlingame, CA, USA) was used as a secondary antibody, and signals were detected by chemiluminescence using ECL Western Blotting Substrate (Thermo Scientific, Rockford, IL, USA) and visualized using LAS-4000 (Fujifilm, Tokyo, Japan).
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