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44 protocols using anti pkm2

1

Western Blot Analysis of Hypoxia Markers

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Total protein was extracted by the peqGOLD TriFast procedure (Peqlab Biotechnology GmbH, Erlangen, Germany). Proteins were separated on 10% polyacrylamide gels and transferred to polyvinylidene fluoride (PVDF) membranes (EMD Millipore, Billerica, MA, USA). After blocking, the membranes were probed with one of the following antibodies: anti-HIF-1α (BD Biosciences, Franklin Lakes, NJ, USA), anti-HIF-2α (LifeSpan BioSciences, Inc., Seattle, WA, USA), anti-PKM2 (Cell Signaling Technologies, Danvers, MA, USA), anti-PKM2 (Y105; Cell Signaling Technologies), and anti-β-actin (Abcam, Cambridge, United Kingdom). All primary antibodies were diluted 1:1000. Then membranes were incubated with secondary antibodies conjugated with horseradish peroxidase (HRP). Antibody complexes were visualized by enhanced chemiluminescence using an ECL kit (GE Healthcare, Little Chalfont, United Kingdom). An image reader (FluorchemTM IS-8900, Alpha Innotech, San Leandro, CA, USA) was used to visualize and quantify western blot bands. Expression was quantified using band intensity values (in arbitrary units), which were normalized to that of β-actin.
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2

Profiling Protein Acetylation and O-GlcNAcylation

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Cells and tumors were lysed in a 1% Nonidet P-40, 50 mM Tris-HCl, 150 mM NaCl, 0.1 mM EDTA buffer with protease, protein phosphatase, and O-GlcNAcase inhibitors. Proteins were immunoprecipitated by incubating whole cell lysates/tumor homogenates with the indicated antibodies for 2 hours and precipitating with Protein A/G agarose beads. Whole cell lysates/tumor homogenates and immunoprecipitation samples were subjected to 8% SDS-PAGE gel electrophoresis and transferred to PVDF membranes. Membranes were incubated with the indicated primary antibodies overnight at 4°C. Western blots were visualized using HRP-conjugated secondary antibodies and ECL. The following antibodies were used: anti-actin (Sigma), anti-acetyl-lysine (AcK, Cell Signaling), anti-Flag (Sigma), anti-HN (Clontech), anti-OGT (Cell Signaling), anti-OGA (Novus), anti-O-GlcNAc (RL2, Abcam), and anti-PKM2 (Cell Signaling).
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3

Profiling Protein Acetylation and O-GlcNAcylation

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Cells and tumors were lysed in a 1% Nonidet P-40, 50 mM Tris-HCl, 150 mM NaCl, 0.1 mM EDTA buffer with protease, protein phosphatase, and O-GlcNAcase inhibitors. Proteins were immunoprecipitated by incubating whole cell lysates/tumor homogenates with the indicated antibodies for 2 hours and precipitating with Protein A/G agarose beads. Whole cell lysates/tumor homogenates and immunoprecipitation samples were subjected to 8% SDS-PAGE gel electrophoresis and transferred to PVDF membranes. Membranes were incubated with the indicated primary antibodies overnight at 4°C. Western blots were visualized using HRP-conjugated secondary antibodies and ECL. The following antibodies were used: anti-actin (Sigma), anti-acetyl-lysine (AcK, Cell Signaling), anti-Flag (Sigma), anti-HN (Clontech), anti-OGT (Cell Signaling), anti-OGA (Novus), anti-O-GlcNAc (RL2, Abcam), and anti-PKM2 (Cell Signaling).
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4

Western Blot Analysis of Cellular Signaling

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Cell lysates were standardized for protein content, resolved on 4% to 12% SDS polyacrylamide gels, and blotted onto nitrocellulose membranes. Membranes were probed with rabbit anti-pPKM2, anti-PKM2, anti-CHOP, anti-GRP78/BIP, anti-pEGFR (Y1086), anti-EGFR, anti-LC3B-I/II, and anti-β-actin (Cell Signaling). Antibody binding was detected by using an ECL Chemiluminescence Kit (Thermo Scientific).
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5

Western Blot Analysis of Tissue Lysates

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Tissue lysates were generated from flash-frozen ground whole tissue or tumors following lysis with ice-cold RIPA buffer supplemented with HALT phosphatase and protease inhibitors (Thermo-Scientific, PI-78420 and 87786). Protein concentrations of the cell lysates were quantified using the DC protein assay kit (Bio-Rad, 500-0112). Next, 15 μg of total protein was separated on 4%–12% Bis-Tris gradient gels (Life Technologies) by SDS-PAGE and then transferred to nitrocellulose membranes. The following antibodies were used for immunoblotting: anti-β-tubulin (1:10000; Sigma, T4026), anti-Hsp90 (1:10000; BD Biosciences, 610418), anti-γ-H2AX (1:1000; Cell Signaling Technology, 9718) anti-PKM1 (1:5000; Cell Signaling Technology, 7067), and anti-PKM2 (1:5000; Cell Signaling Technology, 4053).
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6

Immunohistochemical Evaluation of Tumor Markers

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Consecutive 3-μm sections were cut from each block and subjected to immunohistochemical staining with the EnVision+DualLink system (Dako, Carpinteria, CA, USA). An immunoperoxidase technique was applied following antigen retrieval with microwave treatment (95 °C) in citrate buffer (pH 6.0) for 45 min. Anti-PKM1 (Abgent, San Diego, CA, USA), anti-PKM2 (Cell Signaling Technology, Danvers, MA, USA), HIF1α (Thermo Fischer Scientific, Waltham, MA, USA), and anti-Ki-67 antibody (DAKO) diluted at 0.5 μg/mL were used as primary antibodies. After 2 h of incubation at room temperature, the sections were incubated with a secondary antibody for 30 min. The specimens were color-developed with diaminobenzidine (DAB) solution (Dako) and counterstained with Meyer’s hematoxylin (Sakura Finetek, Tokyo, Japan). Immunostaining of all samples was performed using the same conditions of the antibody reaction and DAB exposure. Immunoreactivities of PKM1 and PKM2 were classified according to the Allred’s score (AS) [50 (link)]: grade 1 for AS = 0, 2 for AS = 2–4, and 3 for AS = 5–8. Grade 2 and 3 cases were regarded as immunopositive [5 (link)]. We also observed 20 microscopic fields per case at 200× magnification and counted the tumor cells per case; the results were expressed as the percentage of tumor cells, with positive nuclei defined by Ki-67 and HIF1α LI [10 (link)].
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7

Western Blot Analysis of Metabolic Enzymes

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Cell lysates were prepared and subjected to WB analysis as performed previously51 (link),52 (link). The following commercial antibodies were used: anti-β-actin (Sigma A1978), anti-PKM2 (Cell Signaling Technology 3198S), anti-PKM1 (Cell Signaling Technology 7067), anti-PKM (Abcam AB118499), anti-human specific LDHA (Cell Signaling Technology 2012S), anti-LDHB (Abcam AB75167), anti-human and rabbit LDHA (Abcam AB135396), anti-p70 S6 kinase (Cell Signaling Technology 2708T), anti-calreticulin (Cell Signaling Technology 12238T), anti-golgin (Cell Signaling Technology 13192), anti-COX IV (Proteintech 11242-1-AP), anti-GPT2 (Santa Cruz sc-398383), anti-PHGDH (Sigma HPA021241), and anti-PC (Santa Cruz sc-271493), horseradish peroxidase-conjugated secondary antibodies anti-mouse (Fisher PI31430) and anti-rabbit (Fisher PI31460). All the primary antibodies were used at a 1:500 dilution in 5% non-fat milk in TBST. Secondary antibodies were used at a 1:3000 dilution in 5% non-fat milk in TBST.
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8

Immunoblotting Analysis of PKM2 Oligomers

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Monocytes and macrophages were collected and lysed in lysis buffer (50 mM Hepes, pH 7.4, 50 mM, NaCl, 1% Triton X-100, 5 mM EDTA, 1 mM PMSF, 10 g/ml aprotinin, 10 g/ml leupeptin, 10 mM sodium pyrophosphate, 50 mM sodium fluoride, and 1 mM sodium orthovanadate). Nuclear proteins were extracted using NE-PER Nuclear and Cytoplasmic Extraction Reagents (Thermo Fisher Scientific). Nonreducing conditions were applied for the detection of PKM2 dimeric and tetrameric forms. For the detection of oligomers, cells were treated with 5 mM of di-succinimidyl suberate (Thermo Fisher Scientific) for 30 min before lysis. Lysates were separated by SDS-PAGE, transferred to nitrocellulose membranes, and incubated with the following antibodies: anti-PKM2 (Cell Signaling Technology), anti-GAPDH (Santa Cruz Biotechnology, Inc.), anti-Lamin A/C (Genentech), horseradish peroxidase-conjugated anti-Ig (Santa Cruz Biotechnology, Inc.), and IRDye 800CW anti-Ig (LI-COR Biosciences). The enhanced chemiluminescence detection system (GE Healthcare) was used to detect bands with peroxidase activity, or membranes were scanned with an Odyssey fluorescence scanner (LI-COR).
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9

Western Blot Analysis of Metabolic Enzymes

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Cell lysates were prepared and subjected to WB analysis as performed previously51 (link),52 (link). The following commercial antibodies were used: anti-β-actin (Sigma A1978), anti-PKM2 (Cell Signaling Technology 3198S), anti-PKM1 (Cell Signaling Technology 7067), anti-PKM (Abcam AB118499), anti-human specific LDHA (Cell Signaling Technology 2012S), anti-LDHB (Abcam AB75167), anti-human and rabbit LDHA (Abcam AB135396), anti-p70 S6 kinase (Cell Signaling Technology 2708T), anti-calreticulin (Cell Signaling Technology 12238T), anti-golgin (Cell Signaling Technology 13192), anti-COX IV (Proteintech 11242-1-AP), anti-GPT2 (Santa Cruz sc-398383), anti-PHGDH (Sigma HPA021241), and anti-PC (Santa Cruz sc-271493), horseradish peroxidase-conjugated secondary antibodies anti-mouse (Fisher PI31430) and anti-rabbit (Fisher PI31460). All the primary antibodies were used at a 1:500 dilution in 5% non-fat milk in TBST. Secondary antibodies were used at a 1:3000 dilution in 5% non-fat milk in TBST.
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10

Quantitative Protein Expression Analysis

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Cell lines were lysed in RIPA buffer [50 mM Tris (pH 7.4), 150 mM NaCl, 1% Triton X-100, 1% sodium deoxycholate, 0.1% SDS, and sodium orthovanadate, sodium fluoride, EDTA, leupeptin, etc.] with protease inhibitors and the total protein concentration was quantified with BCA assay (Thermo Fisher Scientific, Waltham, MA). The normalized samples were analyzed by SDS-PAGE and western blot using standard protocols and the following primary antibodies: anti-PKM1 (1:1,000 dilution, sigma, SAB4200094), anti-PKM2 (1:1,000 dilution, Cell Signaling, 4,053), and anti-actin (1:2,000 dilution, Cell Signaling, 4,970), the secondary antibodies: Anti-rabbit IgG, HRP-linked antibody (1:3,000 dilution, Cell Signaling, 7,074). Results are represented as mean and s.e.m. of at least three independent experiments.
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