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12 protocols using hif 1a

1

Signaling Pathways in Liver and AML12 Cells

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The rat livers and AML12 cells were lysed by RIPA buffer, separated by 10% polyacrylamide gel electrophoresis and then transferred to polyvinylidene fluoride (PVDF) membrane. After blocking in 5% Bovine Serum Albumin (BSA), the membrane was incubated with the phospho-JAK2 (Tyr931) (1:1,000, affinity), total JAK2 (1:1,000, proteintech), phospho-STAT3 (Tyr705) (1:1,500, abcam), total STAT3 (1:2000, abcam), IL-6 (1:500, bioworld), IL-18 (1:2000, bioworld), IL-1β (1:500, sino biological), TNFα (1:1,000, sino biological), HIF-1a (1:1,000, Novusbio), HIF-2a (1:1,000, Cell Signaling Technology), VEGFa (1:1,000, Novusbio) primary antibody seperately overnight at 4°C, and then was incubated with HRP conjugated secondary antibody for 1 h at room temperature. Western blots were displayed by advanced enhanced chemiluminescence kit and then semi-quantified by Clinx (Shanghai Qinxiang Scientific Instrument Co., Ltd).
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2

Immunohistochemical Analysis of Tumor Markers

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Sections of tumor tissue blocks were cut onto adhesive-coated glass slides (Instrumedics, Hackensack) at a thickness of 3 μm. The slides were dewaxed in xylene and rehydrated through a graded alcohol series. Then, slides were pressure-cooked in 10 mM citrate buffer (pH 6) for 7 minutes for antigen retrieval and washed using TBS with 0.1% Tween 80 for 5 minutes. Endogenous peroxidase activity was blocked by 3% H2O2 treatment. After washing, the slides were incubated with primary antibodies against KIT (Epitomics), MAP1LC3B, HIF1A (Novus Biologicals), and PECAM1 (BD Biosciences) at RT for 1 hour. Primary antibodies were detected following the user's manual of the ChemMate DAKO EnVision kit (DAKO). The slides were incubated with the secondary antibody for 30 minutes and developed with 3,3-diaminobenzidine for 5 minutes. Slides were then counterstained with hematoxylin. Incubation without the primary antibody was used as a negative control.
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3

Western Blot Protein Analysis

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Western blot was performed as previously described30 (link). GAPDH was used as a loading control. Uncropped blots can be seen in Supplemental Fig. 4. Antibodies and dilutions used are as follows:
GAPDH (Cell Signaling, 2118, 1:2000)
Phospho-STAT3 (Cell Signaling, 9131, 1:1000)
STAT3 (Cell Signaling, 30835, 1:1000)
HE4 (Origene, TA307787, 1:2000)
HIF1A (Novus, NB-100–134SS, 1:200)
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4

Western Blot Analysis of Angiogenic Factors

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Samples were solubilized in lysis buffer [20 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium dodecyl sulfate (SDS), 1 mM phenylmethylsulfonyl fluoride, 1μg/ml leupeptin, and 2 μg/ml aprotinin] for 1 h at 4°C. The lysates were then clarified by centrifugation at 15,000 g for 30 min at 4°C, were diluted in Laemmli sample buffer containing 2% SDS and 5% (v/v) 2-mercaptoethanol, and were heated for 5 min at 90°C. The proteins were separated via SDS polyacrylamide gel electrophoresis (PAGE) using 10% or 15% resolving gels followed by transfer to nitrocellulose membranes (Bio-Rad, Hercules, CA) and then probed with antibodies against HIF-1a (Novus), CD31 (Abcam), HGF (Santa cruz), VEGF (Abcam), and FGF2 (Abcam) for 1h at room temperature (Table 2). Peroxidase-conjugated anti-mouse IgG or anti-rabbit IgG and enhanced chemiluminescence (Amersham Pharmacia Biotech, Piscataway, NJ) were used as described by the manufacturer for detection. The membranes were scanned to create chemiluminescent images that were then quantified with an image analyzer (Kodak).
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5

Protein Expression Analysis in Tissues

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Samples were solubilized in lysis buffer [20 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium dodecyl sulfate (SDS), 1 mM phenylmethylsulfonyl fluoride, 1μg/ml leupeptin, and 2 μg/ml aprotinin] for 1 h at 4℃. The lysates were then clarified by centrifugation at 15,000 g for 30 min at 4℃, were diluted in Laemmli sample buffer containing 2% SDS and 5% (v/v) 2-mercaptoethanol, and were heated for 5 min at 90℃. The proteins were separated via SDS polyacry-lamide gel electrophoresis (PAGE) using 10% or 15% resolving gels followed by transfer to nitrocellulose membranes (Bio-Rad, Hercules, CA) and then probed with antibodies against HIF-1a (Novus), CD31 (Abcam), HGF (Santa cruz), VEGF (Abcam), and FGF2 (Abcam) for 1 h at room temperature (Supplementary Table S2). Peroxi-dase-conjugated anti-mouse IgG or anti-rabbit IgG and enhanced chemiluminescence (Amersham Pharmacia Biotech, Piscataway, NJ) were used as described by the manufacturer for detection. The membranes were scanned to create chemiluminescent images that were then quantified with an image analyzer (Kodak).
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6

Transcriptional Regulation Profiling

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ARRB1 (A1CT, a gift from Professor R. Lefkowitz), p300 Santa Cruz rabbit polyclonal (sc-585), H3K4me1 Diagenode rabbit polyclonal (pAb-037-050), H3K4me3 rabbit polyclonal (pAb-003-050) and HIF1A Novus Biologicals rabbit polyclonal (NB100-134SS).
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7

Immunofluorescence Analysis of HIF-1α and YAP

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Cells cultured in six-well plates were rinsed three times with phosphate-buffered saline (PBS) and fixed in 4% polyformaldehyde for 15 min. After permeabilization with 0.5% Triton X-100 for 10 min, cells were blocked with 0.1% BSA for 30 min at room temperature. The cells were incubated with the primary antibody (HIF-1a, 1:200, Novus, NB100-105) overnight at 4°C. After rinsing, cells were incubated with Cy3-conjugated goat anti-mouse IgG (H+L) (1:100, Boster, BA1031) for 1 h at room temperature. Following rinsing with PBS, cells were blocked with 0.1% BSA again and incubated with the primary antibody (YAP, 1:200, CST, #14074) and the secondary antibody FITC-conjugated goat anti-rabbit IgG (H+L) (1:100, Boster, BA1105). We counterstained the cells using DAPI (Solarbio, C0065, China) and visualized them under a fluorescence microscope (Olympus, Japan).
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8

Protein Extraction and Western Blot Analysis

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Proteins were extracted in RIPA buffer in the presence of protease inhibitors (Roche). Protein concentration was estimated by the BCA assay (Thermo Scientific). For each sample, 20 μg of protein were resuspended in sample buffer and electrophoresed in a precast 4%–20% Tris gel (BioRad). After gel transfer to polyvinylidene fluoride (PVDF) membranes using a BioRad Criterion system, blots were blocked in 5% nonfat milk/1x TBST for 1 h at room temperature and incubated overnight at 4 °C with the following primary antibodies: Hif1a (Novus Biologicals: NB100479) at 1:1 000, and α-tubulin (Cell Signaling: #2125) at 1:10 000. The membranes were then incubated with a HRP-conjugated anti-rabbit IgG (Santa Cruz: sc-2004) at 1:2 000 for 1 h at room temperature in 5% no-fat milk/1x TBST. The signal was detected by using enhanced chemiluminescence (ECL Prime Western Blotting System GE Healthcare, RPN2232). Western blot images were acquired and analyzed via the BioRad Image Lab system. Quantification was performed using ImageJ. The α-tubulin signal was used to normalize for protein amount.
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9

Western Blot Analysis of Epigenetic Regulators

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Following passage, cells were first washed with PBS before being lysed with fresh RIPA buffer and centrifuged at 10,000× g for 10 min at 4 °C. Total protein concentration in the supernatant was measured using the BCA protein kit (Sigma-Aldrich). Western Blot analysis was performed on 30 μg of protein using DNMT3B (R&D System/MAB7646, Secondary Anti-mouse IgG-HRP, Cell Signalling/70765, London, UK, TET1 (ThermoFisher/GT1462, Secondary Anti-mouse IgG-HRP, Cell Signalling/70765, London, UK, HIF1A (Novusbio/NB100-479, Secondary Anti-rabbit IgG-HRP Cell Signalling/70745, London, UK, HIF2A (Novusbio/NB100-122, Secondary Anti-rabbit IgG-HRP Cell Signalling/70745), and GAPDH (Merck/MAB374, Secondary Anti-mouse IgG-HRP, Cell Signalling/70765, London, UK). The immunoreactivity bands were subjected to UpLight HRP chemiluminescent substrate solution (Uptima) and imaged using a FluorChem M Imager.
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10

Apoptosis Detection and Protein Analysis

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Apoptotic cells were detected using the One Step TUNEL Apoptosis Assay Kit (Beyotime, China). After incubating with the TUNEL reagent in the dark for 1 h at 37°C, cells were stained with 4¢,6-diamidino-2-phenylindole (DAPI, Solarbio, China) for 5 min. Apoptotic cells showed red fluorescence (Cy3 labeled). Images of multiple cells from three independent experiments were obtained with a fluorescence inversion microscope (Olympus, Japan). Beyotime, China) and phosphorylase inhibitor (Servicebio, China). Protein concentration was determined using a BCA protein assay kit (Beyotime). Then, cell lysates were separated by SDS-PAGE (Beyotime) and transferred to PVDF membranes (Millipore). Blots were incubated overnight at 4°C with the following primary antibodies: HIF-1a (1:500, Novus, NB100-105), caspase-3 (1:1000, Proteintech, 19677-1-AP), Bcl-2 (1:1000, Abcam, ab196495), Bax (1:1000, CST, #2772), YAP (1:1000, CST, #14074), p-YAP Ser127 (1:1000, CST, #13008), and b-actin (1:1000, CST, #3700). Immunoblotting was detected using the UVP ChemiDoc-It Imaging System and enhanced chemiluminescence detection kit (Affinity; KF003).
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